Index: the last one

1. November 11, 96, a review on SCAI
   
2. November 22, 96, a review on DSC software (for prediction of protein 2nd structrue) and its Web site
   
3. November 28, 96, Some Softwares for 3D viewing

Week of November 11, 1996

Computational Molecular Biology study in

Research Department of Discrete Algorithms and Applications, SCAI

Institut fur Algorithmen und wissenschaftliches Rechnen in Germany

Some good research works in the area of molecular bioinformatics and computational chemistry have been done in this department.

1. Their publications can be found in Web.
   
• These papers below are what I am interested:
• Koch, I.; Lengauer, T.; Wanke, E.:
  An Algorithm for Finding all Common Subtopologies in a Set of Protein Structures
  Journal of Computational Biology 3,2 (1996)

In this paper, they developed a new fast algorithm which can find all common subtopologies in a set of protein structrues. Thus their work could be used for the comparison and analysis of protein structures, and motif definition and structure classification. This method may help me to analyses the S15a interactor which has unknown function but has homolog to some domains of cytoskeletal proteins (copied).

• Lengauer, T. and Rarey, M.:
  Computational methods for biomolecular docking
  Current Opinion in Structural Biology 6, 402-406 (1996)

A review for substantial progress of recent years in computer-based analysis of biomolecular docking, which will help the understanding of molecular interactions. Protein-protein docking, protein-ligand docking, protein-DNA and protein-RNA docking have been discussed in this review. Among them, protein-protein docking will help me to generate the whole idea about protein-protein interaction, related to my research and/or general protein-protein interactions in the cell. (copied)

• Rarey, M.; Kramer, B.; Lengauer, T.:
  Time-efficient docking of flexible ligands into active sites of proteins
  In: Third International Symposium on Intelligent Systems for Molecular Biology ( C. Rawlings et al., eds.), AAAI Press, 1995

No abstract can be found in 3rd ISMB Web page, but this paper might have the similar feature to the next published paper.

• Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G.:
  A Fast Flexible Docking Method using an Incremental Construction Algorithm In: Journal of Molecular Biology 261,3 (1996), p 470-489

In this paper, an automatic method for docking small organic ligands into protein binding sites has been presented. Their FLEXX chemical model is fast enough for screening ligands. 19 known protein-ligand compleses taken from the PDB had been tested. This paper should be studyed in detail to get a better idea for protein-protein interaction model(s)(copied).

• Vingron, M.; Waterman, M.S.:
  Sequence alignment and penalty choice: review of concepts, case studies and implications
  Journal of Molecular Biology 235 1-12 (1994) (Abstract from Entrez)
  

A review paper on two tools, one is a algorithm to calculate the entire set of optimal alignments under all choices of one or two parameters; Another is the statistical behavior of optimal alignment scores. A better understanding of the dependence of alignments on parameters in general has been gained, they said. This paper might have some help in protein structure prediction with alignment method.

2. There research projects can be viewed in Web
   The following projects might be interesting to us:
• Molecular Bioinformatics:
1. PROTAL - Proteins: sequence, structure and evolution
   A big project dealing with:
   
1. Proteins Sequence, Structure, and Evolution.
   
2. Structure Prediction and Accurate Alignment of Protein Sequences and Structures.
   

Using ToPlign as software, which can be used to predict protein structure

2. PROTEIN - Analysis and prediction of protein structures
   
• Development of algorithms and computer programs to the analysis of known protein structures, prediction of elements of the secondary and supersecondary structure, and retrieval and comparison of protein structure topologies.
  
• Basic research in bioinformatics.
  

I do not know their progress yet.

3. RELIWE - Calculation and prediction of receptor ligand interactions
   In this project, the binding process (molecular docking) between small organic molecules (ligands) and a special protein molecule (receptor) has been studyed. Two softwares have been developed:
1. FlexX is a program for automatic prediction of receptor-ligand interactions.
   
2. FlexS is a program for automatic Structural Alignment of small organic molecules.
   

With their model system, I hope I can expand their ideas to protein-protein (two big molecules) interaction study.

Week of November 22, 1996

A review on

DSC: Discrimination of Protein Secondary Structure Class

with Ross D. King & Michael J.E. Sternberg

This work has been done in Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, UK

There are also some other modelling softwares in this institute, like PREPI (Protein Representations Interactively), a Molecular Graphics package for the display of proteins and nucleic acids, etc.. Their USEFUL LINKS to other "Combi" will be also useful to all of us.

DSC is based on multiply-aligned homologous sequences with an overall per residue three-state accuracy of ~70%. For single sequence, it will find and align homologues and then perform secondary structure prediction by DSC. The program code is free and is in /fvr/molbio/protein. When you are under this directory, run with "dsc input output" (the makefile is ok for skribe/DEC now, the old makefile is copied as MAKEFILE_ORIGNAL). You can also find readme and MANUAL there for help.

I have tryed this program with two of my proteins. I can not check their accuracy yet, however, we can get some ideas from their paper and code.

Identification and application of the concepts important for accurate and reliable protein secondary structure prediction
Protein Science (1996) 5: 2298-2310 (copied)

Week of November 28, 1996

Some softwares for viewing biomolecules in three dimensions on the Net (The information below is useful in future when we need to use them. More will be added here if I find any. But I'll only exam them when I only need to do so.)