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ProSAS

http://services.bio.ifi.lmu.de/ProSAS

Description :
Protein Structure and Alternative Splicing: effects of alternative splicing events on protein structure

PRTAD

http://www.math.iastate.edu/prtad

Description :
PRTAD is a dedicated database and structural bioinformatics system for protein analysis and modeling. The database is developed to host and analyze the statistical data for protein residue level "virtual" bond and torsion angles, based on their distributions in databases of known protein structures such as in the PDB Data Bank. PRTAD is capable of generating, caching, and displaying the statistical distributions of the angles of various types. The collected information can be used to extract geometric restraints or define statistical potentials for protein structure determination. PRTAD is supported with a friendly designed web interface so that users can easily specify the angle types, and retrieve, visualize, or download the distributions of the angles as they desire. PRTAD is freely accessible at http://www.math.iastate.edu/prtad.

Aknowledgement :
The work is partially supported by the research funds provided by the Department of Mathematics, the Graduate Program on Bioinformatics and Computational Biology, and the Lawrence Baker Center for Bioinformatics and Biological Statistics at Iowa State University, the New Faculty Startup Fund provided by the Ogden College of Science and Engineering of Western Kentucky University, and the NIH/NIGMS grant R01GM081680.

References :
1. Wu, D., Cui, F., Jernigan, R., and Wu, Z. (2007) PIDD: Database for Protein Inter-Atomic Distance Distributions. Nucleic Acids Res. 35 (Database issue): D202-D207
2. Feng, Y., Kloczkowski, A., Jernigan, R. (2007) Four-body contact potentials derived from two protein databases to discriminate native structures from decoys, Proteins: Struct. Funct. Bioinf. 68(1): 57-66

CoC Central

http://kulibin.mit.edu/coc/

Description :
The Conservatism of Conservatism (CoC) database presents statistical analysis of the conservation of residue positions in folds across protein families. Residues with high CoC are conserved in families of homologous proteins that acquire the same fold. Such residues can be different in non-homologous proteins (analogues) that exhibit the same fold, but the common conservation points to the general importance of the residue positions. We calculate and present the statistical significance of such conservation and highlight residues that are more conserved than expected given the residue s solvent accessibility. Such high CoC residues have been shown to be crucial for the kinetics and/or thermodynamics of protein folding, are involved in folding nucleation, and are often identified in positions of functional importance such as "super-sites". More information is available at the website (http://kulibin.mit.edu/coc/).

SDR

http://paradox.harvard.edu/sdr

Description :
Predicted specificity-determining residues in protein families

SuperSite

http://bioinformatics.charite.de/supersite

Description :
Dictionary of binding sites in proteins

TMFunction

http://tmbeta-genome.cbrc.jp/TMFunction/

Description :
We have developed the database TMFunction, which is a collection of more than 2900 experimentally observed functional residues in membrane proteins. Each entry includes the numerical values for the parameters IC50 (measure of the effectiveness of a compound in inhibiting biological function), Vmax (maximal velocity of transport), relative activity of mutants with respect to wild type protein, binding affinity, dissociation constant, etc., which are important for understanding the sequence-structure-function relationship of membrane proteins. In addition, we have provided information about the name and source of the protein, Uniprot and Protein Data Bank codes, mutational and literature information. Furthermore, TMFunction is linked to related databases and other resources. We have set up a web interface with different search and display options so that users have the ability to get the data in several ways. TMFunction is freely available.

PhyloFacts

http://phylogenomics.berkeley.edu/phylofacts/

Description :
The PhyloFacts resource contains pre-calculated structural and phylogenomic analysis of over 15,000 protein family "books" across the Tree of Life. Each book includes a multiple sequence alignment, one or more phylogenetic trees, predicted subfamilies, predicted 3D protein structures, active sites and other key residues, cellular localization, and Gene Ontology (GO) annotations and evidence codes. PhyloFacts includes hidden Markov models for classification of user-submitted (DNA or protein) sequences to protein families and subfamilies. Our current focus is on covering all the gene families represented in the human genome and all structural domains, but plan to expand the resource to include all proteins in all species. PhyloFacts enables biologists to avoid the systematic errors associated with function prediction by homology through the integration of a variety of experimental data and bioinformatics methods in an evolutionary framework.

Aknowledgement :
This work was supported by a Presidential Early Career Award for Scientists and Engineers (PECASE) from the National Science Foundation, and by an RO1 from the National Human Genome Research Institute of the NIH.

References :
1. Krishnamurthy, N., Brown, D., Kirshner, D. and Sjölander, K. (2006). PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification. Genome Biology, 7(9):R83.

Protein Segment Finder

http://ari.stanford.edu/psf

Description :
A tool for identification of protein segments obeying a set of primary, secondary, and tertiary structure constraints

FCP

http://cgl.imim.es/fcp/

Description :
Tools and resources for translating the remarkable growth witnessed in recent years in the number of protein structures determined experimentally into actual gain in the functional coverage of the proteome are becoming increasingly necessary. We introduce FCP, a publicly accessible web tool dedicated to analyzing the current state and trends of the population of structures within protein families. FCP offers both graphical and quantitative data on the degree of functional coverage of enzymes and nuclear receptors by existing structures, as well as on the bias observed in the distribution of structures along their respective functional classification schemes.

References :
1. R. García-Serna, L. Opatowski, J. Mestres. (2006) FCP: Functional Coverage of the Proteome by Structures. Bioinformatics 22: 1792-1793

Heme Protein Database

http://heme.chem.columbia.edu/heme.php

Description :
Heme types, protein structures, axial ligands and Em values

AS-ALPS

http://as-alps.nagahama-i-bio.ac.jp/

Description :
Alternative Splicing-induced Alteration of Protein Structure

AutoPSI

http://www.bio.ifi.lmu.de/AutoPSIDB

Description :
Automated structural classification of protein sequences

CC+

http://rainbow.chm.bris.ac.uk/arty/search/

Description :
A resource for elucidating sequence-to-structure relationships for coiled-coil folding and assembly

ColiSNP

http://yayoi.kansai.jaea.go.jp/colisnp

Description :
Mapping non-synonymous SNPs on protein structures

ConSurf-DB

http://consurfdb.tau.ac.il/

Description :
Sequence conservation profiles of the proteins of known structures

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