| Directory > Science > Biology > Biochemistry and Molecular Biology > Biomolecules > Proteins and Enzymes > Structure 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/
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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
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Chromatin Structure and Function
Information regarding histones, histone modifications and their biological roles, and related
links.
http://www.chromatin.us/chrom.html
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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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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/
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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/
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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/
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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
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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
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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
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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/
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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
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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
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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
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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/
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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
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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
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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/
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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/
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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/
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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/
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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/
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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/
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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/
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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
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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/
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ProtoMap
An attempt to classify all proteins from SWISSPROT and TrEMBL into groups of related proteins.
http://protomap.cornell.edu/intro.html
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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/
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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/
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