Web Directory

» 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/

» Biozon
   An attempt to classify all proteins to create a unified biological knowledge resource with emphasis on protein and DNA characterization and classification.
   http://www.biozon.org/

» BlueTB Molecules
   Mycobacterium tuberculosis database with information on DNA sequence, map position, structure, and function of proteins. Includes references to a scientific articles.
   http://bluetb.drpi.ch/

» Chicken Egg White Lysozyme
   Enzymatic activity, sequence, crystallization, 3D structure and links to publications on this enzyme.
   http://lysozyme.co.uk/

» Chromatin Structure and Function
   Information regarding histones, histone modifications and their biological roles, and related links.
   http://www.chromatin.us/chrom.html

» Databases
   Several protein databases including TIMBAL, HOMSTRAD, CREDO, ESST and BIPA including references, maintained by the Department of Biochemistry, University of Cambridge, UK.
   http://www-cryst.bioc.cam.ac.uk/databases

» 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 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/neb/inteins.html

» Kinase.com
   A resource on protein kinases, a key class of regulatory proteins. Includes genomic and evolutionary analyses, classification, disease associations and an extensive database of protein kinase genes.
   http://www.kinase.com/

» Macromolecular Structure Database
   Resource for the deposition and validation of newly proposed structures, maintained by research group, within the European Bioinformatics Institute, Hinxton, UK.
   http://www.ebi.ac.uk/msd/

» 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

» NIGMS: Protein Structure Initiative
   PSI is a federal, university, and industry effort aiming to reduce the costs and time taken to determine a 3D topology. Includes details of funding and featured publications from Bethesda, Maryland.
   http://www.nigms.nih.gov/psi/

» NIGMS: The Structures of Life
   Introduction to structural biology, its relationship to health, disease and developing new medications. Maintained by the National Institute of General Medical Sciences, Bethesda, Maryland.
   http://publications.nigms.nih.gov/structlife/

» 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/

» NetOGlyc 3.1 Server
   Produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian glycoproteins. Maintained at the Center for Biological Sequence Analysis, Technical University of Denmark.
   http://www.cbs.dtu.dk/services/NetOGlyc/

» 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

» 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/

» 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 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/

» Protein Design
   News and discussion in the area of folding, synthesis, and tertiary topology prediction, run by David Yee from Paramount, California.
   http://www.proteindesign.com/

» 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, USA.
   http://www0.nih.go.jp/mirror/Kinases/

» 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/

» 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://www.predictioncenter.org/

» 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

» 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/

» 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/

» 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