CPBS 7711 links

General computational biology sites

• UCHSC's Center for Computational Pharmacology and Bioinformatics Ph.D. program information
• International Society for Computational Biology

• Journals

  • PLoS Computational Biology
  • Bioinformatics (journal)
  • Journal of Computational Biology
  • Journal of Biomedical Informatics
  • BMC Bioinformatics
  • Statistical Applications in Genetics and Molecular Biology

• Conferences

  • Pacific Symposium on Biocomputing Conference site with free full text proceedings.
  • Intelligent Systems for Molecular Biology (ISMB) with free online conference proceedings. Also, the announcement for the 2010 conference
  • RECOMB 2010 conference
  • Rocky Mountain Regional Bioinformatics Meeting

Lecture-related web sites

Molecular Biology Databases

• NAR annual compilation of Molecular Biology Databases
• National Center for Biotechnology Information (NCBI) and specific NCBI sites:
  • Site Map & Educational resources especially the tutorials
  • Entrez (search everything) and Entrez Gene (curated compilations by gene)
  • BLAST (sequence-based searches)
  • PubMed (the biomedical literature, with links to holdings in the UCHSC library)
• UniProt (curated protein information, includes SwissProt and TrEMBL).
• PDB (protein structures)
• InterPro (protein families and motifs)
• The Gene Ontology (molecular biology conceptual structure, with mappings to particular genes), see also OBO
• Santa Cruz "Golden Path" (configurable human genome browser)
• DIP (database of interacting proteins) and MINT, a competitor.
• Kyoto Encylopedia of Genes and Genomes (KEGG) (metabolic and signalling pathways)
• Enzyme DB (US mirror) (enzyme activities), and Reactome, a human-specific competitor. Also consider MetaCyc
• The Human Genome Nomenclature Committee (HGNC) for gene names.
• The Human Protein Reference Database (HPRD)
• Regulatory information databases, such as Transfac, COMPEL, Jaspar, and Mapper, EPD and CREB
• Information Hyperlinked over Proteins (IHOP) generated by text mining.

Database Search and Sequence Alignment

• Various lecture notes on Dynamic Programming, from: GWU's computer science class
• A basic Java Applet demonstrating various sequence alignment algorithms
• BLAST
• code for computing PAM (Point-Accepted Mutations) using Dayhoff matrices

Multiple Sequence Alignments

Remember, none of these are optimal, so looking at the various different alignments they produce can be useful.

• ClustalW2 progressive MSA program
• DCA Divide and Conquer MSA
• DALIGN block based MSA
• Tmsa, IBM's pattern based MSA
• FSA (source code), a method for multiple alignment of large genomic sequences.
• STRAP, a structurally-oriented MSA site.
• Lots of useful MSA programs and links

Hidden Markov Models

• SAM, an HMM creation tool, with documentation, a web server, and a download page. NB: you must fill out and return a free (as in beer) academic license form to download it.
• HMMer, a similar HMM creation tool, with documentation and free (as in GPL) downloading
• Pfam A protein family database built with HMMs.

Protein Structure Prediction

• PDB, the database of protein structures.
• Protein fold class databases. Each uses somewhat different definitions of a class
  • SCOP (First major classification)
  • CATH (most used in CASP, and most current)
• The CASP site, including the most recent CASP8
• LiveBench a continuous assessment of many fully automated prediction approaches
• Automated prediction servers you can use:
  • Robetta
  • BioinfoBank / 3D-Jury
  • Inub
  • Desmond
• The PyMol program (and python libraries) for protein structure visualization and comutation.

Molecular Mechanics, Dynamics and Docking

• The Amber Molecular Simulation Programs, including energy minization and molecular dynamics. $400 for Academic license
• The Charmm (or this version may be more up to date). The competitor from Harvard (Karplus's lab). $600 academic license. Another useful Charmm-related site from Charlie Brooks (see his home page for more useful information).
• Computational Center for MacroMolecular Structures which distributes good free software, including docking
• AutoDock (Open Source)
• FlexX, which has changed licensing terms recently, and is now $1500 for US academic users. A time-limited (8 week) license is available free.
• DOCK (free for academic use).
• 3D-DOCK suite, aimed at protein-protein interactions. Open source or free (beer) for academics.
• Mark Gerstein's movies of molecular dynamics. Try exploring the database of large scale molecular motions
• Arthur Olson's Autodock movies, and the Biotin binding to Streptavidin example.