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Protein Structure

My Thesis: Improvement of Greer's Algorithm for Protein Backbone Modeling

ABSTRACT
Two approaches are commonly used to build protein backbone models for protein crystallography: the skeletonization approach and the topological approach. Among the algorithms implementing skeletonization, Greer's algorithm is a popular one. From our testing, however, some problems exsit in Greer's algorithm. This thesis addresses two of the problems and provides methods to improve the performance of Greer's algorithm.
One problem in the implementation of Greer's algorithm is the limitation of the thinning algorithm it used: Hilditch's thinning algorithm. The thinning method cannot thin a thick shape well. We developed two methods to address the problem: density-reuse and multiple-loop algorithms. Both methods can effectively eliminate the voxel clusters in the skeleton.
The other improvement of Greer's algorithm is to adopt some methods from the topological approach to improve the chain correctness. We convert the skeleton grid from Greer's algorithm to a skeleton graph. The skeleton graph is then used as the input of the FORR cognitive architecture, which is from the topological approach. Usually the backbone is among the most repeatable paths from the evaluation system in the topological approach. From our testing, this integrated method can improve the chain correctness significiantly (up to 99%).

Thesis in pdf format
Thesis in ps format
Thesis Proposal power point slides show
Chap 1: Introduction
Chap 2: Background: Protein Structure Analysis
Chap 3: Implementation of Greer's Algorithm
Chap 4: Improvement of Greer's Algorithm
Chap 5: Conclusion
Source code:
Thin.java | Trace.java | Voxel.java | DVoxel.java
Compare.java | MSAback.java   | Segment.java | Atom.java
OpenGL -- 3-D display compare.c | display.c
Unix Script: allrun run Thin.java etc for a list of proteins
    1a0b.1.07 Sample Parameter File for protein 1a0b: 1A, 0.7 density
    allgrid or generate_thinParam to generate Parameter File for thinning
    allmsa and runmsa run integrated approach for a list of proteins

How to use...

/cis/grad/ableson/bin/generate_grid_edm2    Generate grid for an arbitary space of EDM, by Alan. Unix Script: allgrid
/cis/msa1/ableson/msa/generate_grid_edm2 /cis/msa2/ableson/index/1a0bp.pro minx maxx miny maxy minz maxz 1.0 1a0b.1.grid
      1.0: exact grid interval in A
       .pro: index file
      .grid: output file
/cis/grad/ableson/bin/generate_grid_edm    Generate grid for a unit cell of electron density map, by Alan
generate_grid_edm /cis/msa2/ableson/index/1a0bp.pro 1.0 1a0b.1.grid
      1.0: rough grid interval in A
       .pro: index file
      .grid: output file
/cis/msa2/ableson/bin/solution_coverage    match peaks and passes with PDB data. Unix Script: allcoverage
Run the following three programs:
1.   atom_peak_assoc /cis/msa2/ableson/index/1a0b.pro /cis/msa2/ableson/assoc/1a0b.assoc
      Produce the atomic association file to .assoc
2.   correct_path /cis/msa2/ableson/index/1a0b.pro /cis/msa2/ableson/assoc/1a0b.mdx0.4
      Eliminate the low density passes.
      0.4: density threshold for the passes.
      Density range of each protein can check database status (Passes: min 0.80...) from Alan.
3.   solution_coverage /cis/msa2/ableson/index/1a0b.pro
      Calculate the match.

Links to this lab

MSA Protein Critical Point Database From Alan Ableson
Janice Glasgow's Homepage Boss of the lab
Max's MSA site
Hamish Carr Any question on openGL, ask him:)

Links to others

DataBase:
Protein Data Bank (PDB) Official site for protein structure database
Structural Classification of Proteins Database (SCOP) To select proteins from different protein families that have the structural similarity.
Macromolecular Structure Related Resources from PDB
Structures' graphics in the PDB from Gerard's homepage

Amino Acids and Protein:
Amino Acids their chemsitry formula, structures
Principles of Protein Structure Using the Internet Good tutorial
Tutorial on Peptide and protein Structure by J.E.Wampler, 1996
Protein Architecture

Crystallography and Software:
Crystallography 101 A introduction course on crystallography
IUCR International Union of Crystallography
Crystallography Software links from PDB
CNS software for protein structure refinement with tutorial
Sharp for phase determination
Expasy ProtParam tool for alignment with the known protein
O software for protein structure determination
CCP4 software a collection of disparate programs for macromolecular crystallography
ARP/wARP for improvement and objective interpretation of EDM
Solve by Tom Terwilliger
Raster3D for displaying of protein structure using data from PDB

Paper online:
Databases in Protein Crystallography By Gerard J. Kleywegt & T. Alwyn Jones, Acta Cryst. D54, 1119-1131, 1998
3D Skeletonization /Volume Thinning
Shape papers collections For 2-D, 3-D graphics processing collection
Bibliographical Notes References & Summaries by Frederic F. Leymarie
Links Collection:
Macromolecular Crystallography Links an extensive listing of crystallographic software . Public software for the IRIX systems. Journals.

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