Bioinformatics & Genomics
Companies, Publishers, & Books
Compendiums & Lists of Resource Links
Compounds & Enzymes
Educational & Information Resources
Genomics & DNA Sequence Analysis
Hidden Markov Models
Major Sites & Organizations
Metabolic Pathway Databases & Related
Molecular Modeling & Visualization
Motif, Domain, Profile, Pattern, & Repeat Searches
Multiple Alignment & Phylogeny
Protein & Nucleic Acid Search Servers
Protein Analysis from Sequence
3-D Structure Prediction
Protein Data Bank (PDB)
Searches of PDB
Secondary Structure Prediction & Assignment
Sites with Multiple or Integrated Tools
Software Catalogues, Lists, & Downloads
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A. C. R. Martin Bioinfo Site
Downloadable Java software for bioinformatics, including a Needleman-Wunsch program and a protein structural least-squares fit program.
Analytical Biostatistics Section
[NIH] The ABS offers downloadable software and servers in the areas of sequence analysis, protein structure prediction, ligand binding, and gene expression.
[Univ. of Wisconsin] “A Repository for Data from NMR Spectroscopy on Proteins, Peptides, and Amino Acids.” The database includes information on each biological molecule, NMR spectral parameters, kinetics, thermodynamics,and structure.
Biomolecular Structure and Modelling Group
[University College London] The BSM group brings together people who derive protein and carbohydrate structure information using crystallography or NMR, those who manage databases of this information, and analysts and modellers who examine these structures to try to derive principles of protein folding. Services are offered in the areas of protein sequence and stucture analysis. The group is the home of the CATH protein structure classification database.
EVA: Evaluation of Automatic protein structure prediction
[Columbia University] The EVA service provides a continuous, fully automated, and statistically significant analysis of the accuracy of protein structure prediction servers.
GeneCensus Genome Comparisons
[Yale University] This site provides genome and phylogenetics related information, databases, and services for many classes of organisms, mainly microscopic.
[University of Cambridge] JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features.
[Columbia University Bioinformatics Center] This server submits your protein sequence to other servers through one interface. Analyses are in the areas of protein structure and function.
Molecular Docking Web
[Home page of Dr. Garrett M. Morris] Ligand-protein docking, with access to AutoDock program, important for drug design. Many links for ligands, protein structure, drug design, computational chemistry, bioinformatics.
Molecular Structure Computer Programs
[University of Lunds] Several program packages dealing with molecular structure analysis and NMR data analysis.
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[S. Hubbard & J. Thornton, UMIST] A stand alone program that calculates the accessible area of a molecule from a PDB format file. It can calculate the atomic and residual accessiblities for both proteins and nucleic acids.
[EMBL] Permits the user to submit a sequence for prediction. Links to other pages for multiple sequence alignment, prediction of secondary structure, prediction of solvent accessibility, prediction of transmembrane helices, prediction of topology for transmembrane proteins, fold recognition by prediction-based threading, and evaluation of secondary structure prediction accuracy.
[Berkeley University] PRESAGE is a collaborative resource for protein structure. It provides a database of proteins, each of which has a collection of annotations reflecting current experimental status, structural assignments models, and suggestions.
[University College London] “Promotif analyzes a protein coordinate file and provides details of the structural motifs in the protein.”
Protein Analysis & Modelling Software
[University College London] Publicly available bioinformatics software. Most of these programs are for the analysis of protein sequence and structure.
Protein Modelling Software
[National University of Singapore] Well-annotated links to software for protein modelling programs and their online manuals.
Protein Sidechain Webpage
[Fox Chase Cancer Center] This site links together several sites with information about protein sidechains. These sites contain information on sidechain
conformational analysis, sidechain rotamer libraries, and sidechain conformation prediction.
Protein Topology Home Page
[EBI] This site offers services devoted to protein structural topology and protein topology cartoons.
[ExPASy] An extensive annotated list of links to tools that provide analysis of protein sequences and structures.
[BIMS] Sequence-conformation-structure database for amino acid residues in proteins.
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[The Barton Group] A suite of programs for the comparison and alignment of protein three dimensional structures. The suite will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position.
[Dunbrack Group, Fox Chase Cancer Center] A large list of annotated links to resources in 3-D, structural biology, sequence databases and analysis tools, protein information, home pages of other research groups, and more.
TOP and MAPS
[Lund University] Pairwise/multiple alignment and similarity searches in databases for three dimensinal protein structures.