Bioinformatics: Comparative protein modelling

Saturday, February 18, 2006

Comparative protein modelling

Comparative protein modelling uses previously solved structures as starting points, or templates. This is effective because it appears that although the number of actual proteins is vast, there is a limited set of tertiary structural motifs to which most proteins belong. It has been suggested that there are only around 2000 distinct protein folds in nature, though there are many millions of different proteins.

These methods may also be split into two groups:

Homology modelling is based on the reasonable assumption that two homologous proteins will share very similar structures. Given the amino acid sequence of an unknown structure and the solved structure of a homologous protein, each amino acid in the solved structure is mutated, computationally, into the corresponding amino acid from the unknown structure.

Protein threading scans the amino acid sequence of an unknown structure against a database of solved structures. In each case, a scoring function is used to assess the compatibility of the sequence to the structure, thus yielding possible three-dimensional models.

1 comment:

Anonymous said...: There are also other prediction methods such as "Ab initio" etc.Your blog is very informative[!],why can't you keep it active with many postings so that the visitors could benefit from it?; Tuesday, March 28, 2006 10:29:00 PM

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Some important links to quench your thirst for knowledge in bioinformatics

Biological Databases

Bibliographic:
- SeqAnalRef , sequence analysis bibliography, Expasy.
- BIOBOB , Biocomputing biliography.
Software:
- The BioCatalog
- Yellow BAGI
- Archives for Biological Software and Databases Around the World .
- MolBiology Software , List of software for molecular biology.
Multi-databases browsers:
- ACNUC .
- SRSWWW ( Oslo , EBI )
- NIH GenoBase .
Protein sequences:
- SWISS-PROT .
- OWL .
- PIR .
Protein structures:
- SCOP .
- PDB (RCSB) .
Nucleotide sequences:
- EMBL , EBI.
- GenBank , NCBI.
- DDBJ , Japan.
Transcription factors:
- TRANSFAC
Patterns/families:
- PROSITE
- Pfam
- PRODOM .
- BLOCKS .
- PRINTS .
- Domo .
- ProtFam ( MIPS homepage ) .
- SBASE , Segment BASE.
- PROCLASS
Structure based classifications:
- Tree classification of PDB (by Alexandrov and Fischer using SARF2 ).
- CATH Protein Structure Classification
- SCOP Structural Classification of Proteins.
- PDB chain clustering produced by Fischer et al.
Misc.:
- FlyBase
- GeneCards
Lists of databases:
- LiMB (gopher).
- BioDatabases List .
Longer list

Online Visualization Tools

Genome Channel

Online Programes

Pratt - pattern discovery online
Expression Profiler - online tool for expression profile clustering and sequence pattern discovery
Database searches , EBI ( Fasta , Blitz ,...).
Database searches at DISC (Japan) -- includes Fasta, BLAST, MPsrch and SRS Fasta
Biologist's Control Panel (Baylor college of medicine).
BCM Search Launcher searches, alignments.
SAM , Sequence alignment and modeling system (using HMMs).
Match sequence against PROSITE .
AMAS Analysis of multiple alignments (Geoff Barton).
MSA, Clustal W multiple sequence alignment.
PredictProtein , Heidelberg.
PSA , Protein Sequence Analysis: fits a structure model to your sequence.
Sequence analysis tools , PDB, including multiple sequence alignment .
MEME , motif discovery tool.
Block Maker , at Fred Hutchinson Cancer Research Center.
Bioinformation Search Center
Longer list

Tools

J-Express , a tool for analysing microarray gene expression data
Clustal W , multiple sequence alignment
Phylip , phylogenetic analysis.
Pratt , pattern discovery.
GCG , Wisconsin Sequence Analysis Package Program Manual.
PROPHET , UNIX based software package for data analysis.
RasMol , free program which displays molecular structures.
MolScript , program for creating molecular graphics in the form of PostScript plot files.
PairWise and SearchWise , Ewan Birney's excellent tools for sequence alignment and search.
MEME , Multiple EM for Motif Elicitation

Bioinformatics Sites

EMBnet node in Oslo .
RNA World
EBI , the EMBL Outstation Hinxton.
EMBL , Heidelberg.
EMBnet , the European network for molecular biology.
BIOSCI , Bionet electronic newsgroups.
CBS , Center for Biological Sequence Analysis, Technical University of Denmark.
Expasy , Geneve.
BIBISERV , Bielefeld University Bioinforrmatics Server.
Nee-How , The Bioresource Finder
BSM , Biomolecular Structure and Modelling at UCL.
Human Genome Project Information
Sanger centre , Hinxton, England.
SEQNET , Daresbury, England.
The Johns Hopkins University BioInformatics Web Server.
W. M. Keck Center for advanced training in computational biology.
B3E , Bioinformatics in France.
UK MRC HGMPRC UK Human Genome Mapping Project Resource Centre.
NCBI National Center for Biotechnology Information (USA).
NLM National Library of Medicine (USA).
CGATBSS , Canadian Genome Analysis & Technology (CGAT) Bioinformatics Support Services.
DDBJ DNA data bank, Japan.
GDB Genome Data Base.
ANGIS Australian National Genomic Information Service.
ANU Bioinformatics Hypermedia Service .
HUM-MOLGEN Human Molecular Genetics.
BioMOO The Virtual Meeting Place for Biologists
BioBox , Finland.
Information theory and molecular biology , Tom Schneider's group.
ISREC (Swiss Institute for Experimental Cancer Research), Bioinformatics Group.
DoubleTwist
WWW in Biology , bionet.software.www.
UCSC Computational Biology .
Bioinformatics and Computational Biology at George Mason University .
Computational Biology USC , University of Southern California.
HUJI , Hebrew University of Jerusalem Hadassah Medical School: The Genomic and BioInformatics Server.
Centre of Bioinformatics , Peking.
Bioexchange.com

Papers

Books on bioinformatics
Primer on Molecular Genetics , including glossary .
Recipe book for molecular sequence analysis (ANGIS).
Protein Sequence Alignment and Database Scanning , Geoff Barton
Introduction to sequence comparison , Keith Robison.
Biocomputing Survival Guide
EMBnet Biocomputing Tutorials
Biocomputing Tutorials from EMBnet.
Virtual School of Natural Sciences at the Globewide Network Academy :
- Biocomputing for everyone , from the VSNS (includes Biocomputing in a nutshell ).
- BioComputing WWW course at the VSNS Virtual School of Natural Sciences
- Principles of protein structure WWW course .

Courses in Computational Biology

Advanced Papers

SAM , Sequence alignment and modeling system (using HMMs).
Dirichlet mixtures , improving detection of weak homologies.
Regularizers for estimating amino-acid distributions .
Bill Pearson on homology search .

Journals

Journal of Computational Biology .
Bioinformatics , Bioinformatics Online
CABIOS
Protein Science.
Proteins: Structure, Function and Genetics
Genome Research
Nature , Genome Gateway
Nucleic Acids Research
Journal of Molecular Biology .
The Bioinformer , published by EBI.
In Silico Biology , online journal
PubMed , database of journals.
Bioinform
IDEAL , International Digital Electronic Access Library - online abstracts.

Related Sites

International Society for Computational Biology
The Molecular Biologist's Desk Reference .
The Bioethics Internet Project ,
ELSI , Ethical, legal and social implications of biotechnology.
The DNA files , WWW pages of US radio program series on Human Genome research and its applications.
CBPE , Center for Biotechnology Policy and Ethics.
Eubios Ethics Institute
Is a genome like a computer program , Gary Welz.
DNA Computers , by Yali Friedman.
PhD thesis on DNA computers

Links

Microarray Informatics Resource Page , a collection of literature and web links.
Biolinks from Bioplanet
Biotechnology Software , maintained by The National Biotechnology Information Facility
BRASS , Bioinformatics Resource for Algorithms, Software and Sequences.
Showcase for new WWW servers.
Bio-wURLd .
List at SEQNET
The World-Wide Web Virtual Library: Biosciences , Harvard.
Survey of Molecular Biology Databases and Servers , R. Smith.
Biologists's Control Panel includes searches of many databases.
Pedro's BioMolecular Research Tool.
Amos' WWW links .
Pasteur Institute .
Nee-How , The Bioresource Finder
Web Resources for Protein Scientists , Protein Science.
Motif Bioinformatics Server , Stanford.
Search engine biological Web Sites .
Jeff's biolinks , Yale University.

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