Protein Sequence and Structure Bioinformatics

RCSB PDB Fall 2011 web site update

2011-12-10T16:21:00.001-08:00

Another major website update has been released for the RCSB web site. One of the main new features is Peter's new visualisation of surfaces with the Protein Workshop viewer. The calculation of surfaces is extremely fast and the resulting images look amazing. Here the capsid of a rather large virus (PBCV-1) - PDB ID 1M4X.

To visualize the surfaces, simply launch Protein Workshop from the viewer menu on the Structure Summary page.

Once the viewer has downloaded and installed itself, turn the surface on by dragging the Surfaces handle from Off to Opaque.

There are quite a number of display options, for a more detailed descriptions of all display options view here.

A list of all the new features of the Fall 2011 release, is available on the "what's new page".

Google Scholar Citations Open To All

2011-11-19T10:06:00.001-08:00

This week Google Scholar citations opened up to the public. After the initial release which was providing limited access only, the latest versions is now open for all scientists. What is interesting is that they seem to have created profiles for many scientists in an automated way. While the transparency of this is amazing, I can also imagine that there will be a push-back about privacy issues.

You can check out e.g who are the most cited scientists in Computational Biology or scientists at UCSD or check out Author profiles (e.g. yours truly). At the moment those lists are sorted by number of citations. Would be nice to have a few more sort fields like the already calculated h-index. Another missing feature is an API. Would be nice to be able to script their database and create custom reports.

I believe Google Scholar is setting a new standard for tracking success of scientists and is a serious threat to the ISI web of knowledge.

Google Summer of Code Mentor Summit 2011

2011-10-22T10:28:00.000-07:00

This weekend I am spending at the Google Campus for the Google Summer of Code (GSoC) Mentor summit 2011. Just as in the previous years this is organized as an Unconference, a self-organizing conference without a prepared program. Instead the conference starts with the participants developing the program together. This year is the largest Mentor Summit ever and we are about 100 people over capacity (In total we are more than 300).

Hands up, "Who has edited a Wikipedia page?" almost every hand goes up.

Some GSoC 2011 stats:

This year Google accepted

48 new organisations 175 total orgs

1115 students

There were over 2k mentors

Students from 68 countries

Session Planning

If people want to organize sessions they have 30 seconds to say what topic they want to propose and write the title on a post-it note. The note will be put on a white board. Then people will vote on what sessions they want to attend. Finally the notes on the board are arranged according how the crowd likes.

After two minutes of planning a line is starting to form and many people are excited to propose sessions. Since so many people are proposing sessions the recommendation is to propose only one session per person.

Small selection of topics:

(too many to mention them all)

Wikipedia integration sucks.

How to build a million dollar computing infrastructure for free.

Open source (OS) gaming

How to pass the 5 developer barrier

OS for international development

LibreOffice: How to revive a project

Open Source for open science

How to build your own internet

GSoC What worked what did not work and how to improve next year.

Creating a cover archive for music

How to integrate semantic web into scientific applications

Visualisation of biological networks

Organizing the effort for documentation

How to get students to become long term contributors

Programmer oriented web semantics

Forming a non profit, how to fundraise for it

How to do telekinetic control of user interfaces

Refactoring the music industry

What to do if you have 100+ sub-modules

Community building

How to make the experience more local

How geeks give away their power with body language

How to get an keep female developers

Astronomy

Usability

Open source in Asia

Aging project infrastructure

OS in higher education

How goverments can sponsor open source projects

Contribute to Openstreetmap

Detailed Program
http://gsoc-wiki.osuosl.org/index.php/2011
https://docs.google.com/spreadsheet/ccc?key=0AsVnlPsfrhUIdHZPVTlpMWJOZ3JwSHlFOURObEVMWnc#gid=0

Some Pictures

I like the built-in power plugs in the meeting room tables

The Google Tyrannosaurus

Session - Integrating Creative Commons content

Demo: software to create music videos from Flickr.
Problem: nobody can get attributions right.

Flickr has 200 million CC images. However they are not all using the same variation of CC. Different types of CC are not compatible with each other.

now commenting on Etherpad:

http://etherpad.osuosl.org/integrating-creative-commons-content

Open Science Session
http://willyou.typewith.me/p/gsoc-open-science

Your Wikipedia Integration Sucks
http://etherpad.osuosl.org/IIAp0hzoid

Sunday

Cycling at the Google campus

Non-Profit Infrastructure for Software Freedom
http://etherpad.osuosl.org/im9y39OyFm

Fundraising 101 ("Free as in Freedom So Who Pays for the Beer?")
http://etherpad.osuosl.org/VK23qSKZCb
- plan
- don't depend on only one sponsor
- types of sponsors: indivduals, small businesses in community, businesses that use your software, local, foundations
-per-feature fundraising (-sometimes, be careful)
- What does a sponsor want to buy? - don't sell your email list. not everything is for sale. Virtue, in some cases forgiveness. Hiring
- And what are you prepared to sell? - ads on website, sponsored emails. Non-profits might have tax issues with certain types of ads. (depending on how they look)
- How to find sponsors. Ask everybody, look at your logs, use your mailing lists, be create, brave, hear no, be tenacious.
- Prepare your elevator pitch. Can you explain the benefit of your project in one sentence to an eight year old. Include your contact information. Make it easy to help. For events: plan and be realistic.
- Ask for help and offer help.
- Build a relationship, they might be able to connect you with somebody else who can sponsor.
- Make it easy to contribute, have a "donate now" button. Accept credit card, send thank you email.
- Enable Microdonations
- How to get graphic help. You need to go to where the artists are.

At lunch: a drone, remote controlled from a phone:

Walking around the campus

How to build your own Internet using open wireless

http://willyou.typewith.me/p/gsoc-openwireless

RCSB PDB web site September update

2011-09-15T20:17:00.000-07:00

This week the latest update to the RCSB PDB web site went life. One of the major new features in this release is a new search interface. Alex has redesigned the top bar search box:

If you enter a search term, the new auto-suggest box provides suggestions what you might mean and allows to trigger precise searches, which are powered by an efficient new lookup mechanism in the background (written by Dimitris).

If you are not happy with the suggestions that you see (I can hardly imagine that ;-), you can still press enter and do the full text search across the PDB, which has been there already before.

Another major new feature of this release are the improvements to the PDB101, the educational section of the site. Proteins that are described in more detail as part of the Molecule of the Month articles, now have a Discussed Structure page. A particular nice detail that I want to point out is Greg's new 3D molecular viewer that works on iPhones and iPads. These gadgets usually can't display Jmol, our standard 3D viewer, due to the lack of Java support. To work around this limitation there is now a new HTML5-sprite base animation. If you access a Discussed Structure page with a mobile device this is displayed and can be rotated left-right by "moving" it with your finger. Other improvements on the educational section are that the molecule of the month articles now show up in search results and you can download an article onto your phone.

I will describe more new features some other time..

Tabular Report Web Services at the RCSB PDB

2011-08-02T20:06:00.000-07:00

I have fallen behind on describing new features of the RCSB PDB web site... Let me catch up! One of the features that I find useful for people who want to script the site is that each of the queries on the site (and there are many) can be represented by simple XML.

How can you find that XML? Once you have run a query, you can access your query history from the left-hand menu. (We might actually move this to the top in the next release to make this more visible, but that's a different story.) Under the Query Details menu you can find the XML.

Here is an example XML for a query. This one below would simply list all current protein structures.

So what can you do with this XML? You can POST this using the Search Web Services and get back a list of matching PDB IDs for this query. This functionality has been available for a while. As a new feature of the current RCSB PDB website release, Chunxiao extended this service to allow Custom Reports in a few different file formats.

Custom Reports

I have mentioned these reports already in a previous blog entry. On the Web site these reports allow to obtain Image Collages, pre-defined reports containing various fields, and exports to Excel to mention just a few of the available options.

As part of the new Web service these reports allow to fetch various fields via XML, comma separated file, or as an Excel file. There are step by step instructions available for how to use this new feature. Happy scripting!

Google Scholar Citations - Google Scholar Blog

2011-07-26T03:42:00.000-07:00

Google is preparing the release of a new feature at Google Scholar - personalized user profiles. They can be used to track your citations and as a reporting tool for calculating the h-index. The access can be kept private or made public. I believe this can be a serious threat to the ISI Web of Science. Can't wait until I can get access to "My Citations" and play around with this new feature!

Read more at: Google Scholar Citations - Google Scholar Blog

UPDATE: In the meanwhile I got access to the new profile feature. The secret is to click on the "MyCitations" tab in Scholar every now and then, until it works. At the moment it found most, but not all of my papers, with some highly cited ones missing. I will make my profile publicly available, as soon as I have figured out how to add the missing articles.

UPDATE 2: In the meanwhile I figured out how to find the missing articles. Scholar is using groups of citations. In my case my family name with the special character ć lead to two groups of citations, one for an author with and without the accent on the name. Using the import functionality those groups could get merged and my profile is now available from http://scholar.google.com/citations?user=LnXh0T8AAAAJ

PDB101 a new view for educational users

2011-05-03T23:40:00.000-07:00

PDB-101 is a new view of the RCSB PDB molecule of the months that is dedicated for educational users. It groups the molecules of the months into categories that are easy to access. The categories have been chosen so they represent important aspects of a structural view of biology.

April release of RCSB PDB web site

2011-04-20T20:07:00.000-07:00

The April release of the RCSB PDB web site has been made available this week. As usually I am planning to describe some of the most exciting new features in a couple of postings here. First, a quick overview:

PDB-101: Educational Resources for Exploring a Structural View of Biology

Structure Summary Sequence Tab

Advanced Search

Tabular Reports

External Links

BioJava at Google Summer of Code 2011

2011-03-23T18:08:00.000-07:00

The Open Bioinformatics Foundation has again been accepted as a mentoring organization for this year's Google Summer of Code. This means we will be able to offer mentoring through BioJava again this year. Accepted students will get a stipend of 5,000$ from Google. Participation is possible from most countries in the world, as long as you are eligible to work in the country in which you'll reside throughout the duration of the program.

If you are interested in working on a BioJava related project, now is the time to start preparing and discussing your proposals. Last year we had many applications for the projects proposed by mentors. If you want to distinguish your application I recommend to propose your own project. Don't forget to discuss any proposal with us before you submit them. We will try to provide feedback and match you with a suitable Mentor.

Also see http://biojava.org/wiki/Google_Summer_of_Code and Google's
FAQs: http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs

The student application deadline is April 8th. Google will announce which proposals got accepted on April 25th.

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank

2011-03-09T19:55:00.000-08:00

The RCSB PDB web site serves around 165 000 unique visitors per month. Did you ever wonder how a site like this can provide reliable service? Our latest publication Quality assurance for the query and distribution systems of the RCSB Protein Data Bank, describes some of the principles that we apply to ensure quality.

BioJava 3.0 released

2010-12-28T13:27:00.000-08:00

Today we released BioJava 3.0. It is available from http://biojava.org/wiki/BioJava:Download.
Over the last year BioJava has undergone a major re-write. It has been modularized into small, re-usable components and a number of new features have been added. The new approach, modeled after the apache commons, minimizes dependencies and allows for easier contribution of new components.

At the present the main modules are:

biojava3-core: The core module offers the basic tools required for working with biological sequences of various types (DNA, RNA, protein). Besides file parsers for popular file formats it provides efficient data structures for sequence manipulation and serialization.

biojava3-genome: The genome module provides support for reading and writing of gtf, gff2, gff3 file formats

biojava3-alignment: This module provides implementations for pairwise and multiple sequence alignments (MSA). The implementation for MSA provides a flexible and multi-threaded framework that works in linear space and that, as an option, allows the users to define anchors that are used in the build up of the multiple alignment.

biojava3-structure: The 3D protein structure module provides parsers and a data model for working PDB and mmCif files. New features in this release are the implementation of the CE and FATCAT structural alignment algorithms and the support of chemical component definition files, for a chemically and biologically correct representation of modified residues and ligands.

biojava3-protmod: The protein modification module can detect more than 200 protein modifications and crosslinks in 3D protein structures. It comes with an XML file and Java data structures to store information about different types of protein modifications collected from PDB, RESID, and PSI-MOD.

Not every feature of the BioJava 1.X code base was migrated over to BioJava 3.0. A modularized version of the 1.X sources is available as a new "biojava-legacy" project.

New Data Drilldown options

2010-12-13T19:00:00.000-08:00

One of my favorite features that was recently added to the RCSB PDB site is the drilldown of search results. In this release an extension to this was added. It is now possible to drill down through EC numbers as well as through the SCOP classification.

A useful trick, that some people might not have noticed yet is that the drilldown is available for the whole set of PDB entries. By clicking on the total number of entries on top of the page one can access this faceted browsing interface over the whole database. The screenshot below shows where you have to click to access this feature.

After clicking on the total number of entries here is the drilldown for the whole of PDB:

Personal Structure Annotations at RCSB PDB

2010-12-11T10:52:00.000-08:00

The latest RCSB PDB release provides the possibility of attaching personal annotations to PDB entries. If you have been using the iPhone application, you might have noticed that this feature has been introduced there already a few weeks ago. Now you can also annotate your favorite proteins directly at the RCSB PDB website.

How does this work? If you are not logged into myPDB, and you view the details of an entry on the Structure Summary page you will see something like this:

Before you can create an annotation you need to get a MyPDB account and log in. This is possible on the left-hand menu in the MyPDB box:

After logging in you can tag and annotate every entry:

I am using this tool to keep comments and notes on various PDB entries. For the future it would be nice to be able to share those notes with some of my friends or students. Another nice feature for the future would be to be able to attach "positional" features in order to e.g. annotate active sites or domain boundaries.

December 2010 release of RCSB PDB website

2010-12-07T16:44:00.000-08:00

The December 2010 release of the RCSB PDB web site has been made available. Again it contains a set of exciting new features, some of which I am going to describe in more detail during the next follow up postings.

Annotations

  Ligand Features
  Tabular Reports
  Data Drill-down
  Visualization
  General Site Improvements

Bioinformatics manuscript update

2010-11-16T09:38:00.000-08:00

Today Bioinformatics released our paper: Pre-calculated protein structure alignments at the RCSB PDB website. However something has gone wrong and the paper requires registration for access. We requested the open access publishing license when the paper got accepted. I just contacted the editors. Until this is sorted out, you can access the final version of the manuscript for free through these links:

UPDATE: by now the article is correctly available as open access.

NAR database issue 2011, new RCSB PDB paper:

2010-11-01T21:20:00.000-07:00

Our next paper has become public available:

The RCSB Protein Data Bank: redesigned web site and web services

in which we describe our developments at the RCSB PDB web site during the last two years.

http://nar.oxfordjournals.org/content/early/2010/10/28/nar.gkq1021.full.html? ijkey=fKC45N3RRezzpj9&keytype=ref

Hope you find it interesting!

At the Google Summer of Code Mentor Summit

2010-10-23T11:37:00.000-07:00

This weekend I am spending at the Google Summer of Code Mentor Summit. It is a great event hosted at the Google Campus in Mountain View. Below more info about the sessions I am attending.

Sessions:

Overview of all sessions

Student retention

Notes at http://openetherpad.org/student-retention

Measuring Usability

Criteria for usability:

Notes at http://etherpad.osuosl.org/gsoc2010usability

Abstraction Level
Closeness of mapping
Consistency
Diffuseness/terseness
Eror-Proneness
Hard mental operations
Hidden dependencies
Junxtaposability
Premature Commitment
Progressive Evaluation
Role expressiveness
Secondary Notation
Viscosity
Visibility

How to make a team use agile development, if they have never done it before

Notes at: http://typewith.me/agile

Liberate your data
Notes at: http://typewith.me/liberate-data

Sunday ...

Open Streetmap
using Cherokee for quick OSM rendering http://code.google.com/p/cherokee/

Advanced Trolling
(This seems to be the most popular session so far ;-)
Notes at: http://etherpad.osuosl.org/advanced-trolling
http://trolluniversity.com/
the CRAPL license http://matt.might.net/articles/crapl/

Open Source Science

Jim Procter and I organized the Open Source Science session:
http://etherpad.osuosl.org/open-source-science

New Paper: Precalculated Protein Structure Alignments at the RCSB PDB website

2010-10-11T22:16:00.000-07:00

Bioinformatics just made our latest paper available as an early preview:
Precalculated Protein Structure Alignments at the RCSB-PDB website

ABSTRACT
Summary: With the continuous growth of the RCSB Protein Data Bank (PDB), Berman et al. (2000), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user.

Availability and Implementation: A web user interface is available at
http://www.rcsb.org/pdb/workbench/workbench.do. The source code
is available under the LGPL license from http://www.biojava.org.
A source bundle, prepared for local execution, is available from
http://source.rcsb.org

UPDATE: the link below should provide free access:
Read the full paper here

Improved Reporting Features at the RCSB PDB site

2010-10-11T05:22:00.000-07:00

One of the features at the RCSB PDB site that many people are not aware of, is the powerful tabular reporting tool. Any search result can be use to generate one of several reports. (e.g. Image Collages, pre-defined reports, fully customizable tables, export to Excel, etc. see screenshot below).

In this release Chuxiao added better reporting for Ligands. There are also plenty of new options for the fully customizable reports, based on feedback we have received from our users.

BioJava's Google Summer of Code summary

2010-10-08T06:00:00.000-07:00

Today a slighlty belated summary of what happened at the Google Summer of Code at the BioJava project:

Our two students Mark Chapman and Jianjiong Gao did an amazing job on their two projects "All Java Multiple Sequence Alignment" (MSA) and "Identification and Classification of Posttranslational Modification of Proteins" (PTM).

For Multiple Sequence Alignments we now have a flexible and multi-threaded MSA implementation that works in linear space and that, as an option, allows the users to define anchors that are used in the build up of the multiple alignment. The code is available as part of the new biojava3-alignment module.

The Posttranslational Modification module (biojava3-protmod) can detect three different types of protein modifications in protein structures. It comes with an XML file & Java data structures to store information about different types of protein modifications, and contains entries from RESID, PDBCC and PSI-MOD. There is also a visualisation component to display cross linked PTM on a sequence viewer.

Both Mark and Jianjiong have expressed their interest in maintaining and further developing their modules and I am looking forward to interacting more with them in the future. I want to thank the Mentors and Co-Mentors Peter Rose, Kyle Ellrott and Scooter Willis for their help and guidance for the projects, without them this would not have been possible. Thanks also to Robert Buels and the Open Bioinformatics Foundation for organizing our applications for GSoC and last, but not least, Google for sponsoring this Summer of Code.

New iPhone app at RCSB PDB (beta)

2010-10-07T06:00:00.001-07:00

The latest RCSB PDB release features a first version of an iPhone application. It is provided as a HTML5-based application, which means you can install it without going to the Apple Store. Simply point your iPhone Safari-browser to http://www.pdb.org and click "yes" a couple of times. Best to do this while you are on a wireless connection, since the application installs some data for quicker data access.

Gregg, the author of this application also made a screencast with the installation instructions. You can watch it here:

New RCSB PDB Feature: Faceted Browsing

2010-10-06T06:00:00.000-07:00

One of the features I find most exciting at the latest RCSB PDB web site release is "faceted browsing". Similar to an online shopping site, which allows to drill down through product categories, it is now possible to drill down through lists of protein structures using categories like Resolution, Organism, Polymer Type, to name just a few of them.

You can easily start browsing by clicking the total number of structures on top of every page. Since this features has become available (Thanks Dimitris!) I have observed myself to use it all the time and I perform much fewer "advanced queries", because this new feature is so easy and quick to use. Let us know if you want to have additional categories.

October release of RCSB PDB website

2010-10-05T17:00:00.000-07:00

The latest release of the RCSB PDB website features a number of exiting new features some of which I will present in more detail during follow-up blog postings.

Above a screenshot of the new Category Browser for the Molecule of the Months.

Here a list of all new features:

Molecule of the Month Improvements

PDBMobile for the iPhone
Query Result Browser Improvements
Chemical Components
Tabular Report Improvements
Comparison Tool Improvements
General Site Improvements

Getting the most out of the Combinatorial Extension (CE) algorithm

2010-10-04T21:18:00.000-07:00

The CE algorithm is a frequently used algorithm for protein structure alignment. We have recently ported the CE algorithm from C to Java and made the new implementation available through BioJava project. It is run as part of the Protein Comparison Tool at the RCSB PDB web site. This was a good opportunity to learn a few hidden aspects of the original implementation and re-consider some of the parameter choices that have been take for the original code. Here a quick summary of how CE works and how to get the most out of it.

CE essentially has two main steps:

Finding Aligned Fragment Pairs (AFPs) between the two protein structures that share similarity. This step in most cases is quite quick, however this only provides a rough alignment as a result which needs refinement.
The alignment optimization steps is the slow part of the algorithm. It iteratively tries to extend the initial alignment while staying below a certain RMSD threshold.

So how does these two steps work in detail? Today we will look at Step 1:

Step 1: Finding AFPs:This step starts with calculating Matrices of intra-molecular distances withing each of the two proteins. These are matrices that describe the distances within a protein and they look something like this:

Here you can see the two matrices, on the left for the alpha chain of Hemoglobin, and on the right side for the beta chain of Hemoglobin. You can view their alignment at the RCSB PDB web site.

As you can see the two chains are very similar. Their pattern of intra-molecular distances looks similar, too. The regions that are colored indicate close proximity in space. Can you spot the helices?
There are a few different ways to compare such distance matrices. In order to identify the AFPs, CE takes the approach to "slide a window" over each of the matrices and tries to find regions where the two proteins looks similar.

This is how it is calculated: First all distances for fragments of size 8 are calculated and the difference of Distances is

This can be done by calculating differences of distances for each fragment of length winSize, which is one of the parameters that can be sent to CE and which is by default set to a length of 8.

The original CE paper has a table on the impact of this parameter. Here you can see how different values for winSize (here called Fragment size m) affect the final RMSD, alignment length and calculation time.It is impressive how much CPU speed has improved since back in those days: Now the alignment shows up almost instantly on my screen. However back then they only had a 248 Mhz CPU and you can see in the table above how many seconds one had to be patient back in 1998.

I tried to reproduce this table with the current implementation, but the numbers don't show up exactly the same. There were a few follow up publication on the algorithm during which this step got improved. The trace step has now some RMSD threshold parameters which make sure that the RMSD between the traces stay within limits.

In this table the internal numbers after the Step 1: As you can see the main effect is on the nr. of traces that are being detected.

winSize	nr traces	RMSD after initial trace
4	2,662,211	4.4
6	1,858,380	3.8
8	1,158,327	4.6
10	891,807	4.3
12	847,802	4.3
16	758584	4.0
24	261,290	5.0
36	17395	4.6

To come back to the differences of distances between the fragments of length winSize: at this stage the difference of distance matrix looks like this:

Each dot on the matrix corresponds to the start of a fragment and color corresponds to closely similar fragments. As you can see there are plenty of regions that have similar fragments, and the fragments come in groups.

The next step, optimizing the alignment, will be discussed some other time...

New version of RCSB web site released

2010-06-08T17:31:00.000-07:00

The RCSB team just released the next major update of the RCSB PDB web site. Here the main features of this release:

General Site Improvements

Structure Alignment Improvements

Molecule of the Month Improvements

Chemical Component (Ligand) Search Improvements

Tabular Report Improvements

biojava-structure now supports Chemical Component Dictionary

2010-06-01T07:00:00.000-07:00

I have updated the BioJava structure data model to support the PDB
chemical component dictionary. This has the benefit that now

* Chemically modified amino acids can be detected (and treated as
amino acids, rather than Hetatom groups)
* It is possible to get a component type for each Group, which allows
to identify ligands.

As a consequence the nr. of amino acids in a chain can change compared
to the previous data representation. As such the loading of chem.
comps is set to "false" by default. It can be configure by the
"loadChemCompInfo" flag in the PDB/mmCIF file parsers.

PDB ID 1A4W - Thrombin with Thiazole-containing Inhibitors. Image source: RCSB PDB

An example where this representation makes a difference is PDB ID 1A4W. This structure contains several Ligands and a chemically modified residue. Without the help of the Chemical Component Dictionary it would have been difficult to correctly represent this protein.

You can get the code either from BioJava SVN, or from the (still slightly experimental) Maven repository at http://www.biojava.org/download/maven/ .

New Structure Alignment Features at the RCSB PDB Web Site

2010-05-25T16:17:00.000-07:00

With the upcoming new release there will be a couple of new protein structure alignment related features:

*) The RCSB PDB web site is providing a structure alignment service. This service can calculate structure alignment on the server side. It also caches all alignments. This means if you come back the next day you can view the same result quickly.

Preview the new alignment service here:
http://betastaging.rcsb.org/pdb/workbench/workbench.do

*) Circular Permutations (CP) in proteins are difficult for alignment algorithms to detect since they depend on the sequence order. These permutations are re-arrangements of the sequence, resulting in different amino acid connectivity, while conserving the overall 3D shape of a protein. Spencer Bliven has extended the Java version of CE and introduced support for the detection of such permutations. This is achieved by working with an internal representation of the proteins that allows to identify alignments across N and C termini. Since this slows down the calculation about three times, the detection of CP is optional.

View an Example of a Cirularly Permutated protein structure alignment

From multi resistant drugs to multi resistant plants

2010-05-08T09:33:00.000-07:00

I have always been critical about the increasing monoculture in agriculture. The combination of powerful herbicides and special herbicide resistant crop has on one side increased yield, on the other side reduced the diversity of available crop strains.

Similar to the way some diseases adjust to our drugs and become resistant, it seems multi- herbicide resistant plants are now also becoming a problem:

http://www.nytimes.com/2010/05/04/business/energy-environment/04weed.html

This should come to little surprise for anybody who knows a bit of history of modern agriculture. There are other examples of monoculture and how evolution and adaption of nature in the end puts the harvest at risk. The most prominent example to day is the Banana:

Modern bananas are not as sweet as they used to be in the first half of the 20th century. The then dominant Gros Michael banana essentially was extinct due to monoculture and the emergence of a fungus, killing this plant. This happened before the 1960ies, so not many people can remember this today. I have never eaten a Gros Michael banana myself, so I can only cite other sources that claim that Gros Michael was a better tasting fruit than the Cavendish variety we are eating today. The Cavendish is resistant to the fungus that killed Gros Michael, but reportedly not as sweet and creamy.

Here more about the history of the banana:

http://www.naturalnews.com/023339_banana_bananas_disease.html

To come back to the beginning of this blog, the emergence of multi-resistant plants should alert all farmers. Growing a variety of different strains should become a priority again.

Integration of open access literature into the RCSB Protein Data Bank Using BioLit

2010-05-03T20:54:00.000-07:00

In our latest article we describe how we integrate open access articles from PubMedCentral that mention PDB IDs into the RCSB PDB web site. For every PDB entry it is now possible to see how it has been used in the publicly available literature.

http://www.biomedcentral.com/1471-2105/11/220/abstract

On a side note, I am not impressed about the slow pace with which this article got through the review and publication process. It took months to get this out.

New look and feel at RCSB PDB web site

2010-04-01T07:48:00.000-07:00

RCSB PDB has been advised by a worldwide top consultancy about how to take the look and feel to the next level. We are planning to release the result with the next major update. Please take a look and let us know any feedback:

http://betastaging.rcsb.org/pdb/home/home.do

How Google Buzz affects my Blog

2010-03-24T20:47:00.000-07:00

I like Google Buzz, since most of the postings that I can read there are mainly work related. It has also affected my blogging here: While I still don't seem to get many comments on my postings here, it seems people like to comment on Buzz, where this blog is listed as a connected site of my account. I will start adding links to Buzz threads of my blogs in the discussion section.

Converging the different Google technologies would be nice in this case. Google are also owning the site that is hosting this blog. Why can't Buzz threads related to this blog automatically appear here?

The Hadoop Hype

2010-03-18T22:49:00.000-07:00

Currently there is a big hype around Hadoop. Map/Reducing your compute problems is being sold by the effective Amazon marketing department as the solution to all your calculation problems. In principle the concepts are very interesting and certainly useful and applicable for some situations, in particular if you are dealing with large sets of data. Here a few comments that are based on some experiences that we gained during last summer, when we asked a very efficient summer student to investigate how well Hadoop was suited to run a large number of protein structure alignments.

The protein structure alignment problem is limited by the available CPU and not so much a problem of large amounts of data (read below about a bioinformatics problem that behaves differently). The conclusion from last summer is that Hadoop is suited in principle to run structure alignments, since the problem can be Map/Reduced to single pairwise alignments. Still there are a couple of issues that make me skeptical how well Hadoop is suited for other other bioinformatics problems that in a similar way are not so much data intense but limited by CPU or memory:

1) Installation

If you want to start setting up your own Hadoop cluster, be prepared to spend a considerable amount of time with configuring it. The whole installation process is non-trivial. Best to try to convince your sysadmin to do the config for you (if you are lucky enough to have one).

2) Performance impact

The way Hadoop and the built-in distributed file system work, some percentage of the system time needs to be spent for synchronization between the different instances. This means not all the CPU on your system can be used for crunching your data. If you only have a few servers and you want to get the maximum usage out of them, you might be happier with technically simpler approaches.

3) Distributed file system

The distributed file system coming with Hadoop is really cool and rather unique, BUT to get access to the data stored in this file system requires custom and peculiar code. This means you have to write code that is specific for this system and your implementation gets tied to this platform. As mentioned above, the alignment problem is mainly CPU limited. A such the distributed file system is an overkill for the large scale structure alignment problem.

4) Amount of data

If you are confronted with a problem that requires processing of very large amounts of data, you would probably benefit from the distributed file system. But be aware of the limitations of network bandwidth: you will either require your own, in-house Hadoop cluster, or you will have to convince your management to allow you to send your confidential data on several hard disks with FedEx to Amazon. This might be a workable approach in some cases, but I am highly skeptical how this can scale for high throughput data. Next Generation Sequencing technologies are creating terrabytes per day, how do you want to ship those?

5) Does not run in my data center

The Hadoop architecture is not compatible with the setups in data centers that academic researchers like me can easily get access to. Most data centers are using "traditional" job queuing systems that won't play together well with the Hadoop approach. While time might change this issue, for the moment, if I want to use the maximum amount of CPU that I can get relatively cheaply, Hadoop is simply not an option.

We ended up using the Open Science Grid to run up to 1,000 concurrent jobs (100,000 CPU hours). Our simple client-server approach (see details here) is very flexible and the client code can get run pretty much anywhere - anybody who wants to set up a screen saver for it?

Google Summer of Code 2010

2010-03-18T14:43:00.000-07:00

Our (the Open Biology Foundation's) application for the Google Summer of Code has been accepted. http://socghop.appspot.com/gsoc/program/accepted_orgs/google/gsoc2010

I am offering to mentor a project to develop an All-Java Multiple Sequence Alignment algorithm as part of the BioJava project.

If you are an interested and skilled student, take a look at the project description, and if you think you are up for the challenge, send me an email with your application.

http://biojava.org/wiki/Google_Summer_of_Code

Latest release of RCSB PDB web site contains all vs. all protein structure alignments

2010-03-03T07:20:00.000-08:00

Last night we released the latest major version of the RCSB PDB web site. This release contains a number of exciting new features:

All vs. all protein structure alignments

* Interactive Structure Alignment Display
* Expert Mode for Protein Comparison Tool

General Site Improvements

* Home Page Layout and Customization
* OpenSearch Integration
* Resizable Viewer Applets

Query Results Page and Tabular Reports Improvements

* Bidirectional Sorting
* New Image Collage Page
* Report Table Filtering
* One-to-Many Relationships in Report Tables

Ligand Search Improvements

* Ligand Top-Bar Search
* Ligand Advanced Search
* Chemical Structure Search
* Ligand Summary Page

2010-02-26T09:37:00.001-08:00

In our latest publication, we are discussing the benefits of the use of Widgets in bioinformatics and demonstrate a few examples that we are making available from the RCSB PDB website:

Will Widgets and Semantic Tagging Change Computational Biology?

Testing upcoming release of all v.s. all protein structure alignment comparisons

2010-02-16T19:33:00.001-08:00

At RCSB PDB we are currently working on an all vs. all comparison of PDB. A preliminary version of this is available from the betastaging site for public testing. e.g.:

http://betastaging.rcsb.org/pdb/explore/structureCluster.do?structureId=2W72

This is a beta site so it might not always be available or some things might not work as expected, still it should give you a pretty good impression of what is in preparation. If you want to help testing, have a look there and let me know how it goes.

Some documentation on the all vs. all procedure can be found here:

http://betastaging.rcsb.org/pdb/static.do?p=general_information/cluster/structureAll.jsp

BioHackathon 2010

2010-02-11T22:16:00.000-08:00

Currently the BioHackaton '2010 is happening in Japan. The goal is integration of biological resources with Semantic Web technologies. Brad Chapman is blogging about what is going on there. Here links to his blog:

Day 1

Day 2 - Python SPARQL query builder

Day 3 - Fish, interoperating and data retrieval

Day 4 - Improved python SPARQL query interface

Day 5 - The final day

How Informatics can help in a crisis

2010-01-25T05:51:00.000-08:00

Today's blog is not about bioinformatics, but another open-source area in informatics that I feel passionate about: open geographical data. The OpenStreetMap (OSM) project provides free geographic data, such as street maps. It is essentially the wiki of the mapping world. In a response to the recent earthquake disaster in Haithi, OSM started the Project Haiti .

In short time so much data has been collected that what was before a largely empty map is now one of the most complete maps of Haiti. Michael Maron posted some before and after images on Flickr:

Before the earthquake (Jan 12th) :

and by Jan 14th:

Beyond just marking roads, there is also an analysis of damaged buildings and displacement camps. This rendering, taken from the OSM wiki, shows damaged buildings and refugee camps mapped within OpenStreetMap.
A few other geographical projects related to Haiti are described at crisiscommons.org .

Resources:

Project Haiti at OpenStreetMap
Haiti Crisis Map shows the tagging of damaged buildings and camps, also can overlay sattelite images

BioJava Hackathon - Last Day

2010-01-22T08:24:00.001-08:00

Today was the last day of the BioJava Hackathon. It has been an exciting week and we made progress along several lines, which I will talk about in a moment. Special thanks go to Jonathan Warren for organizing the meeting room at the Sanger Institute. Also thanks to our hackers without who this hackathon would not have been possible. In particular thanks to Scooter Willis, Jules Jacobsen, Andy Yates, Jonathan Warren, Christoph Gille, Matias Piipari for participating during the week and to our special guests who joined us for a day, Richard Holland and Jim Procter.

All the code that has been written is available through the new modules labeled with the biojava3 name. Most work was related to the new sequence and protein structure modules:

Sequence modules

There have been a lot of discussions about the current way sequences are represented over the last years. As such the "sequence guys" among the developers were working on coming up with a new design which is providing a biological meaningful (think central dogma) representation of sequences. What is still missing are file parsers using the new modules. The first fasta parser is about to be committed by Scooter as I am writing this. There is still more work required before the code will be ready for the next release. Still this is the beginning of a new data representation which should make the code base ready for the next couple of years.

Structure modules

The protein structure modules are the BioJava3-part which is closest to be released. During this week we have added the CE algorithm for protein structure alignment, implemented core interfaces for a generic Model View Control wrapping of various 3D visualization tools, we added better support for chemically modified residues (like MSE) and natural ones like Selenocysteine. They are treated now as amino acids. We also re-factored the code base to have the structure data model clearly separated from the new graphical user interfaces. This gui module now provides a nice way for calculating and visualizing protein structure alignments.

Next BioJava release (3.0)

There is still more work required to push the new sequence module to a state where it can be released. We also did not write any documentation this week, so that will have to be added later on. We will try to bring up the modules to a state where they can be released over the next weeks. Once a module is release ready a detailed summary of the new features will be posted to the mailing list. In any case there will be a BioJava 3.0 release in time for the ISMB/BOSC conference as we have been doing during the last years.

BioJava Hackathon - Day 3

2010-01-21T07:42:00.000-08:00

Today the various efforts of this week start to come together. We have several new or refactored modules in SVN that contain the code designed and written this week. They are named with biojava3 to clearly indicate that this are the new things.

BioJava Hackathon - Day 3 - Sequence Modules

2010-01-21T01:09:00.000-08:00

Another main feature of the Wednesday session is an update to the sequence modules. Scooter Willis extended the sequence-core modules to provide the framework for working with sequences according to what was discussed earlier. There is still room for tweaks, refactoring and future optimizations but for the most part we can represent DNA,RNA and Protein sequences in a biologically aware manner with minimum code complexity at the top level. Check out the biojava3 package in the sequence-core module.

BioJava Hackathon - Day 3 - Structure Modules

2010-01-20T08:14:00.000-08:00

Today the main new feature in the structure modules is the release of a Java port of the Combinatorial Extension (CE) algorithm. This contains both a version of the algorithm that can be run from command line, as well as a GUI to view the results and trigger custom alignments. Essentially this is what is available from the RCSB website from: http://www.rcsb.org/pdb/workbench/workbench.do

About the generic design for Model View Control for 3D viewers, an unsolved problem is currently how to deal with selections. Selecting ranges, chains or atoms in proteins is done using a scripting interface at PyMol or Jmol. Shall we have a scripting interface (based on the syntax of one of these) or shall we have multiple select methods that accept various arguments? Jules Jacobsen wrapped the Jmol-Biojava interface using the new interface definitions for the MVC.

BioJava Hackathon - Day 2

2010-01-19T09:38:00.001-08:00

Yesterday's contributor who added most lines of code is Michael Heuer, who is joining the hackathon from remote (i.e. somewhere in the US). He added the new FASTQ parser to BioJava. Well done Michael!

During the morning session we did a "Post Up", a silent and structured way of doing brainstorming. This was in order to come up with a new requirement how to do some state of the art pushing on the sequence modules. Scooter moderated a discussion where we focused on biologically meaningful representations of biological sequences. A Chemical Compound will be at the core of any sequence representation and we want to have different types of sequences like Chromosome sequence, Scaffold, DNA, RNA, Protein, and Sugars.

We started with test-driven development for the new sequence interfaces and then we will wrap the existing sequence code with the new interfaces. Here you can see us during the brainstorming session:

On the 3D structure side of things, we added a new 3D structure-gui module that is going to provide the Model View Control interface for the various open source viewers.

BioJava Hackathon - Day 1 part 2

2010-01-18T14:36:00.001-08:00

Continuation of Day 1...

We had more discussion about how to deal with the sequence modules, bytecode dependencies of the core module and related topics. Seems there is a general agreement about moving the current sequence code out of the core module into its own space. Will continue tomorrow morning, when Richard Holland is back.

On a different side of things, Christoph Gille, Jules Jacobsen and I were discussing how to provide a Model View Control interface for using various open source 3D visualization libraries (Jmol, RCSB Libraries, Astex Viewer) together with Biojava.

We spent a lot of time discussing today, hope to be able to get more code done tomorrow.

BioJava Hackathon - Day 1

2010-01-18T08:11:00.000-08:00

Hi,

I am going to blog every day about the BioJava Hackathon, so you can stay updated with what is happening here in Cambridge.

In the morning I gave this presentation around which we had several discussions about what are the most critical issues we want to solve. The issues are:

Installation problems. Getting the latest checkout of the new Maven based build system causes problems for some of us. Sorting our the installation procedure is a major topic of the afternoon. It works successfully with the latest Eclipse, the m2eclipse plugin and subclipse plugin. Some of the NetBeans based developers also reported no problems during installations.
Features. The Biojava features should become a first class citizen. This means it should be possible to instantiate them independently of sequence objects.
Simplify Sequences: Sequences should be Strings as far as possible. Only convert them to Sequence objects if required.
Some of the BioJava 3 docu is not up to date and can lead to misunderstandings. The latest BioJava 3 code is available in the trunk
Memory efficiency: Make sure that iterating over RichSequences is memory efficient. (Fix a memory leak there)
Bytecode: The Biojava - core module should not require the Bytecode module.

Andy Yates is tweeting about it at http://twitter.com/search?q=%23biojava

BioJava Hackathon 2010

2010-01-16T01:00:00.000-08:00

I am off to Cambridge, U.K. where we will have the BioJava Hackathon next week. I am planning to blog on a regular basis about what is going on there.

All vs All Structure Alignments in PDB

2010-01-15T04:14:00.000-08:00

Proteins can have various degrees of similarity. If two proteins show high similarity in their amino acid sequence, it is generally assumed that they are closely evolutionary related. With increasing evolutionary distance the degree of similarity usually drops, but proteins can still show similar function and have an overall similar 3D structure, even if the sequence similarity is low. The detection of such remote similarities is important in order to infer functional and evolutionary relationships between protein families and is a core technique used in structural bioinformatics.

For the RCSB-PDB web site I have recently been working on a new all against all comparison of all protein chains. While protein sequence comparisons can be computed quickly, the calculation of protein structure alignments is much more time consuming. So far we were computing about 140 mio. pairwise alignments in ~100.000 CPU hours on the Open Science Grid (OSG). With the help of Chris Bizon we could easily deploy our code there and I can highly recommend giving the OSG a try also for other scientists. A technical report about how we computed about 140 mio. pairwise alignments in ~100.000 CPU hours is available from here:

http://osg-docdb.opensciencegrid.org/cgi-bin/ShowDocument?docid=919

Protein Comparison Tool

2010-01-10T20:58:00.000-08:00

In the recent months I spent some time developing the new RCSB PDB Protein Comparison Tool (you can see an example for it on the right-hand menu of this blog).

In particular I spent a lot of time porting the CE and FATCAT algorithms from C to Java and developing a new user interface. Check out the latest version at http://betastaging.rcsb.org/pdb/workbench/workbench.do . (E.g. try to align 4HHB chain A and 4HHB chain B ).

Having the algorithms in Java opens the door for a number of nice applications. It is now possible to launch the structure comparison application with a single mouse click using the Java Web Start technology.

BioJava Hackaton

2009-12-29T05:13:00.000-08:00

The BioJava Hackaton will be held from from Jan. 19th-22nd at the Genome Campus, Hinxton, Cambridge, UK.

Our goals are:

- Further development of the BioJava modules. For module specific goals see the Modules pages on the BioJava wiki.
- Anything the module leaders deem necessary for their modules.
- Add new modules
- Finalizing BioJava 3.0

New major release on RCSB PDB web site

2009-11-17T18:06:00.001-08:00

At the RCSB PDB we just released another major update to our web site

New features are

For more details, see the What's New page.

An easy way to set up a web site (using Java, Maven and Eclipse)

2009-09-01T14:18:00.000-07:00

Download the following open source software:

* Tomcat 6 from http://tomcat.apache.org/download-60.cgi
unpack it in a local directory. (I got the Core tar.gz one)

* Eclipse (the JEE edition) from http://www.eclipse.org/downloads/
launch Eclipse

In Eclipse:

* Install the Maven (m2eclipse) plugin for eclipse by adding

http://m2eclipse.sonatype.org/update/

as a new site under Help->Install New Software-> Add

Select the the checkboxes of the modules you want to install.

Create a new Eclipse project

* Select File-> New -> Other -> Maven Project

leave project name and location to the default values

as a project Archetype select maven-archetype-webapp

as a group ID select the name of your organisation e.g. org.biojava

Artifact ID is the name of your module. E.g.: myweb (this will also be in your servlet URL)

This will create the following servlet in your workspace.

Deploy the project on Tomcat

* Add a new Tomcat 6 server : Select File-> New -> Other -> Server

* select Apache-> Tomcat 6

* point it to the location at which you upacked Tomcat

* add your servlet to it and press Finish

* Start your server buy either clicking the green button, or right click on your servlet project and say Run As -> Run on Server

* Tomcat will start and the servlet is running

Add new jsp pages and start the development of your servlet!

Finally: If you want to give the servlet to your sysadmin to release on a production site, just do a Right click on the project and do Run As -> Maven package . This will create a myweb.war in the target subdirectory of your project that can be deployed in stand alone tomcat instances outside of eclipse.

Hydrogen bonds in proteins

2009-08-25T21:37:00.000-07:00

Hydrogen bonds play an important part in determining the 3D structure of proteins. The formation of H-bonds contributes to the stability of a protein. They provide a characteristic pattern in secondary structure elements that can be used for secondary structure assignment.

A hydrogen bond is formed when two electonegative atoms compete for the same hydrogen atom. While the hydrogen is covalently bound to one of the atoms, the donor, it interacts with the other atom, the acceptor. The possibility to interact with one atom, while covalently bound to another, is special for hydrogens. The electrostatic and covalent aspects of the bond cause the three atoms to stay mostly linear.

H-bonds in proteins most frequently involve the C=O and N-H groups of amino acids in the polypeptide chain. A single oxygen can simultaneously participate in two bonds.

Here again some example code that can calculate the energy of an H-bond between the N-H and C=O atoms of two amino acids using BioJava. It assumes that the coordinates for H-bonds were calculated as described in one of my earlier postings.


/** calculate HBond energy of two groups in cal/mol ...
    * see Creighton page 147 f
    *
    * Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997.
    * categorizes hbonds with donor-acceptor distances of
    * 2.2-2.5 Å as "strong, mostly covalent",
    * 2.5-3.2 Å as "moderate, mostly electrostatic",
    * 3.2-4.0 Å as "weak, electrostatic".
    *  Energies are given as 40-14, 15-4, and <4 kcal/mol respectively.
    *
    */


   public  double calculateHBondEnergy(AminoAcid one, AminoAcid two )
   throws StructureException{


      //System.out.println("calcHBondEnergy" + one + "|" + two);

      Atom N = one.getN();
      Atom H = one.getH();

      Atom O = two.getO();
      Atom C = two.getC();

      double dno = Calc.getDistance(O,N);
      double dhc = Calc.getDistance(C,H);
      double dho = Calc.getDistance(O,H);
      double dnc = Calc.getDistance(C,N);

      

      double contact = MINDIST ;

      //   there seems to be a contact!
      if ( (dno < contact) || (dhc < contact) || (dnc < contact) || (dno < contact)) {
         //System.out.println("!!! contact " + one + " " + two);
         return HBONDLOWENERGY ;
      }

      double e1 = Q / dho  - Q / dhc ;
      double e2 = Q / dnc  - Q / dno ;

      double energy = e1 + e2;

    

      // bond too weak
      if ( energy > HBONDHIGHENERGY)
         return 0;

      // test to avoid bond too strong
      if ( energy > HBONDLOWENERGY)
         return energy;

      return HBONDLOWENERGY ;

   }

RCSB PDB releases new version of web site.

2009-08-18T14:44:00.000-07:00

The RCSB has released a new major version of their website.

The main new features are:

For a detailed summary of the new features go to the What's new page.

One of the new Web Widgets is used in the right hand menu of this blog...

BioJava plans for the next months

2009-08-17T07:00:00.000-07:00

Posted this to the BioJava mailing lists:

Here a quick summary of what I propose to be our action plan for the next months for BioJava:

* I would like to call for a code-freeze in 2 weeks (or so) in order to finalize the new modularized and mavenized version of biojava for the developers. The current developmental trunk will remain permanently frozen and all future work should continue at a new location in SVN. As such it will be important that all developers commit any changes they are working on before that.

* We will update the documentation for how to obtain a new mavenized checkout on the wiki.

* After the change the new modules need to be tested and if no major problems are found, the ok will be given to continue working on the new modules (at the new location)

* All developers should obtain a new checkout.

* We need to identify sub-module leaders who will take over leadership of the sub-modules.

In order to come up with a new release of biojava we should continue development on the new modules for a few months. Talking off list with Richard Holland it looks like we will have a hackaton in January in Cambridge, U.K. (details to be finalized and announced). I suggest that we use that opportunity to focus on further developing the modules and make a new public BioJava release shortly after that.

At the present I see the following topics that would be great to work on until and during the hackaton in order to prepare a shiny new version of BioJava for public release:

+ Work on standardizing the organization of the modules (tests, examples, source, docu etc.)
+ Add new modules
+ Improve existing modules
+ Anything the module leaders deem necessary for their modules.
+ Use OSGI for visualization related modules

I can post a more detailed and specific list of things to work on if people are interested.

How to calculate H atoms for Nitrogens in protein structures

2009-08-16T10:06:00.000-07:00

Only few protein structures contain coordinates for hydrogen (H) atoms. This is because X-ray crystallography usually does not resolve the positions of H atoms. They have only one electron and they barely scatter X-rays. Only a few structures have been determined with a high enough resolution to place the hydrogen atoms (< 1.2 Å). Some PDB files contain H atoms that have been modeled into the protein structure. Neutron Diffraction is a method that does allow to observe H atoms. An protein that has been determined with a combination of X-ray and Neutron Diffraction and that contains hydrogen atoms is PDB ID:3HGN .

If hydrogen atoms are required for calculations (e.g. to calculate hydrogen bond energies in protein structures) they need to be inferred from the available information. Here two possible ways to approximate positions for H-atoms that are bound to the Nitrogen (N) atom of an amino acid.

Let's start with having a look at the peptide plane. We can use vectors from the plane in order to calculate H atoms.

A simple way to infer the coordinates is by putting the H on the opposite side of the O atom that is bound to C. C coordinates are from amino acid i. N, Cα atoms from amino acid i+1, for which the H atom is being calculated. For the examples below we are using BioJava. It treats every atom as a vector. This means, if the code fragments below talk about atoms it is meant as a synonym for a vector in a 3D space.


Group a  = groups[i];
Group b  = groups[i+1];

// atom will be for group b.
Atom H = calcSimpleH(a.getC(),b.getN(),b.getCA());

/** Calculates the H atom for group B (i+1) */
private static Atom calcSimpleH(Atom c,Atom o, Atom n) throws StructureException{

Atom h = Calc.substract(c,o);
     double dist = Calc.getDistance(c,o);
     //System.out.println(dist);
     double x = n.getX() + h.getX() / dist;
     double y = n.getY() + h.getY() / dist;
     double z = n.getZ() + h.getZ() / dist;

     h.setX(x);
     h.setY(y);
     h.setZ(z);

     return h;
}

One issue with this first approach is that H is not necessarily directly opposite of the C-O.

An alternative method is shown below:

Use the unit vectors NC and NCα to get the direction of the vector and substract it from N.



Group a  = groups[i];
Group b  = groups[i+1];
Atom H = calc_H(a.getC(),b.getN(),b.getCA());


/**
* Calculates the H atom for group B (i+1)
*/
private static Atom calc_H(Atom C, Atom N, Atom CA) throws StructureException
{

     Atom nc  = Calc.substract(N,C);
     Atom nca = Calc.substract(N,CA);

     Atom u_nc  = Calc.unitVector(nc)   ;
     Atom u_nca = Calc.unitVector(nca);

     Atom added = Calc.substract(u_nc,u_nca);

     //(According to Creighton the distance N-H is 1.03 +/- 0.02 Å.)
     Atom U = Calc.unitVector(added);

     Atom H = Calc.add(N,U);

     return H;
}

If you are doing your own implementation of this I recommend to add a check that the distance N-H is really 1 Angstrom. Additionally write out a modified PDB file and use a 3D viewer to verify that the atom is placed on the correct side of the N.