Molecular interactions
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[edit] Molecular interactions - Web Resources
FireDB is a database of Functionally Important Residues from proteins of known structure, bringing together both ligand binding and catalytic residues in one database. Integrates biologically relevant data from the close atomic contacts in PDB crystal structures and reliably annotated catalytic residues from the Catalytic Site Atlas. Users can query by protein, ligand or keyword. Relevant biologically important residues are displayed in a way that allows users to assess binding site similarity across homologous proteins. Binding site residue variations can be viewed with molecular visualization tools. 
iSPOT
Web tool to infer the interaction specificity of families of protein modules. Infers the recognition specificity of protein module families; it is based on the SPOT procedure that utilizes information from position-specific contacts, derived from the available domain/ligand complexes of known structure, and experimental interaction data to build a database of residueâresidue contact frequencies. iSPOT is available to infer the interaction specificity of PDZ, SH3 and WW domains. For each family of protein domains, iSPOT evaluates the probability of interaction between a query domain of the specified families and an input protein/peptide sequence and makes it possible to search for potential binding partners of a given domain within the SWISS-PROT database. The experimentally derived interaction data utilized to build the PDZ, SH3 and WW databases of residueâresidue contact frequencies are also accessible.
ConsInspector
ConsInspector predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. Computer-assisted prediction, classification, and delimitation of protein binding sites in nucleic acids.
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MHCPred
Server for quantitative prediction of peptideâMHC binding. Accurate T-cell epitope prediction is a principal objective of computational vaccinology. As a service to the immunology and vaccinology communities at large, we have implemented, as a server on the World Wide Web, a partial least squares-based multivariate statistical approach to the quantitative prediction of peptide binding to major histocom- patibility complexes (MHC), the key checkpoint on the antigen presentation pathway within adaptive cellular immunity.
Vakser Lab â GRAMM
Search Vakser Lab. Sections Home. Info. People. Resources. Research. Education. Seminars. Contact Us. Bibliography.. Personal tools. This site conforms to the following standards:. Section 508.. WAI-AAA.. Valid XHTML.. Valid CSS and ...
Index of /
Index of /. Name. Last modified. Size. Description. APBC2005/. 10-Feb-2005 10:53 - ATG/. 30-Jul-2002 14:19 - Ag7/. 23-Jan-2006 13:33 - AllerPred/. 17-Feb-2006 17:17 - AllerTool/. 06-Feb-2006 18:05 - Analysis/. 07-Oct-2005 15:58 - BLAST. ...
ClusPro Server
Filtering, Clustering, and Ranking Protein-Protein Complexes Application: Protein-Protein Docking Web Server Ranking of receptor-ligand complexes using energy filtering and clustering Click here. for documentation, bugs and other ...
BindN for prediction of DNA and RNA binding residues in proteins
BindN for prediction of DNA and RNA binding residues in proteins BindN applies support vector machines (SVMs) to prediction of DNA and RNA-binding residues from sequence features, including the side chain pKa value, hydrophobicity index ...
