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Topology of Protein Structure
Provides articles and FAQ explaining cartoon depictions, atlas of tertiary arrangements of polypeptides within predicted crystal. Includes server for upload of PDB code, and software downloads from University of Leeds, UK.
http://www.tops.leeds.ac.uk/
Structural Classification of Proteins
A key for different proteins based on structural features, with keyword search and PDB data, and an entry viewer for download.
http://scop.mrc-lmb.cam.ac.uk/scop/
Chromatin Structure and Function
Information regarding histones, histone modifications and their biological roles, and related links.
http://www.chromatin.us/chrom.html
Tyrosine Residues in Different Proteins
EPR spectrum of a tyrosyl radical provides information about rotational angle of phenoxyl ring. Database compiled to identify the responsible locus, maintained at the University of Essex, Colchester, England.
http://privatewww.essex.ac.uk/~svist/lev1/tyrdb/home.shtml
Protein Structure and Function (Petsko and Ringe)
3 parts (Prediction of secondary structure, Membrane protein structure and Protein motifs) of chapter 1 (From Sequence to Structure) can be read for free
http://www.new-science-press.com/browse/protein/
ProtoMap
An attempt to classify all proteins from SWISSPROT and TrEMBL into groups of related proteins.
http://protomap.cornell.edu/intro.html
Atlas of Protein Side-Chain Interactions
Modeling the packing of all 20 amino acid side-chains with one-another and with DNA - from Birkbeck and University Colleges, London.
http://www.biochem.ucl.ac.uk/bsm/sidechains/
Sodium and Potassium Transmembrane Pump
Abstract and movie to promote article from Department of Surgery, Universities of Queensland and Otago, Dunedin, New Zealand.
http://www.proinformatix.com/mod.html
Protein Data Bank
PDB provides a text based format for archiving experimentally-determined, three dimensional structures, at the Brookhaven National Laboratory, with list of mirror sites worldwide.
http://www.rcsb.org/pdb/
Principles of Protein Structure
Archive of online course, with discussion lists, and summary of lecture notes from 1996 at Birkbeck, University of London, UK.
http://www.cryst.bbk.ac.uk/PPS2/
Protein Structure and Function
Architecture, folding, solubility and stability, as part of course in enzymology and protein engineering, at the Department of Food Science and Technology, University of Reading, UK.
http://www.fst.rdg.ac.uk/courses/fs916/
Protein Structure Initiative
Large scale attempt to determine topology, through collaborative internet based effort, maintained by Millennium Information, Inc., Cambridge, MA.
http://www.structuralgenomics.org/
CAMPASS
Protein alignments organised as a database of over 5000 protein domains organized into structural superfamilies, including references maintained by the Department of Biochemistry, University of Cambridge, UK.
http://merlin.bioc.cam.ac.uk/~campass/
Protein Structure Prediction Center
Advances and archive of meetings on critical assessment of 3D determination from sequence using alignment tools. Maintained at Lawrence Livermore National Laboratory, California.
http://predictioncenter.llnl.gov/
Macromolecular Structure Database
Resource for the deposition and validation of newly proposed structures, maintained by research group, within the European Bioinformatics Instutute, Hinxton, UK.
http://www.ebi.ac.uk/msd/
Glucocorticoid and Nuclear Receptor Resource
Collection of individual databases on members of the steroid and thyroid hormone and their receptors from Georgetown University, Washington, DC.
http://nrr.georgetown.edu/GRR/GRR.html
Histone Acetyltransferase
Provides a database of proteins that acetylate histones, including links to active researchers in the field and related links.
http://www.cstone.net/~jrb7q/hathome.html
Histone Sequence Database
Compendium of histone protein sequence alignments, including postranslational modifications and proteins containing the histone fold, at the National Human Genome Research Institute, Bethesda, MD.
http://genome.nhgri.nih.gov/histones/
Hydrogen Exchange Mass Spectrometry
Analysis of proteins and protein dynamics with hydrogen exchange and mass spectrometry from Corrales, NM.
http://www.hxms.com/hxms.htm
InBase
Overview of protein splicing, exteins and the intein database at New England Biolabs, Inc. Includes links to publications at the NCBI, National Library of Medicine, Maryland.
http://www.neb.com/inteins/intein_intro.html
Metalloprotein Database and Browser
Resources for coordination patterns, and estimating distance between metal and ligand at binding sites. Includes search and visualization interfaces, maintained by the Scripps Research Institute, La Jolla, CA.
http://metallo.scripps.edu
NetNglyc
N-glycosylation site prediction in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons, from Center for Biological Sequence Analysis, Technical University of Denmark.
http://www.cbs.dtu.dk/services/NetNGlyc/
Peptide Peptidomimetic Informatics
Devoted to the modeling of polypeptide structures, aiming to bridge the gap from organic to biochemistry for undergraduates at the University of Pittsburgh, Bradford, PA.
http://www.pitt.edu/~soriano/peptide.htm
Protein Kinase Resource
Functional and structural information, based on protein sequence, with link to nomenclature for the signaling cascade genes, maintained at the San Diego Supercomputer Center, CA.
http://pkr.sdsc.edu/html/index.shtml
Proteins Under Pressure
Research to provide insights leading to novel engineering and biotechnology applications at Rensselaer Polytechnic Institute, Troy, NY.
http://www.rpi.edu/web/Campus.News/dec_01/dec_03/proteins.html
ProWeb Project
Summarizes features of protein families, documentation to capture biological richness through links to home pages of workers in the field from FHCRC, Seattle, WA.
http://www.proweb.org/
Protein Design
News and discussion in the area of folding, synthesis, and tertiary topology prediction, run by David Yee from Paramount, CA.
http://www.proteindesign.com/
International Association for Protein Structure Analysis and Proteomics
Mission, board members, and bylaws promoting the discovery and exchange of new methods and technique. Includes archivce of meetings, and contacts.
http://faculty.virginia.edu/fox-iapsap/
Rainey, Dr. Jan K.
Publications and tips for dihedral angle calculation, bioinformatics data and scripts for collagen and amino acid side-chain predictions, work using atomic force microscopy, solid and solution state NMR, from Edmonton, Canada.
http://www.pence.ca/~jrainey
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