:: DESCRIPTION
KYG predicts RNA interfaces out of 3D structures of RNA-binding proteins.
::DEVELOPER
Center for Informational Biology, Ochanomizu University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kim, O.T.P., Yura, K., Go, N. (2006)
Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction.
Nuc. Acids. Res. 34 (22), 6450-6460.
:: DESCRIPTION
SigniSite performs residue level genotype phenotype correlation in protein multiple sequence alignments by identifying amino acid residues significantly associated with the phenotype of the data set.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W286-91. doi: 10.1093/nar/gkt497. Epub 2013 Jun 12.
SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.
Jessen LE1, Hoof I, Lund O, Nielsen M.
:: DESCRIPTION
CPORT is an algorithm for the prediction of protein-protein interface residues. It combines six interface prediction methods into a consensus predictor
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
PLoS One. 2011 Mar 25;6(3):e17695. doi: 10.1371/journal.pone.0017695.
CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.
de Vries SJ1, Bonvin AM.
:: DESCRIPTION
Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein–protein interaction hot spots, post-translational modification sites and sequence variability.
::DEVELOPER
Bioinformatics Institute of Singapore.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Kuan Pern Tan; Raghavan Varadarajan; M. S. Madhusudhan
DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr356
:: DESCRIPTION
NADbinder server discriminate the NAD interacting residues and non-interacting residues from a given sequence. The NADbinder server uses the SVM based method by using the Position Specific Scoring Matrix (PSSM) generated from the query sequence(s).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2010 Mar 30;11:160. doi: 10.1186/1471-2105-11-160.
Identification of NAD interacting residues in proteins.
Ansari HR1, Raghava GP.
:: DESCRIPTION
VitaPred is a SVM (Support Vector Machines) based prediction method for the vitamin-interacting residues in protein sequences. Vitamins play vital role in the cell and involves in the various enzymatic reaction and functions as a cofactor. VitaPred predicts that which amino acid residues in the protein sequence will interact with the vitamins. An example of protein-vitamin binding given in the following diagram, where pyridoxal 5′-phosphate (PLP, red color) interacts with specific residues (yellow color) of a protein (cyan color).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2013 Feb 7;14:44. doi: 10.1186/1471-2105-14-44.
Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information.
Panwar B1, Gupta S, Raghava GP.
:: DESCRIPTION
The LnLCorr package is designed to detect pairwise coevolutionary among residues in a set of proteins using likelihood ratio tests.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wang ZO, Pollock DD:
Coevolutionary patterns in cytochrome coxidase subunit I depend on structural and functional context.
J Mol Evol 2007, 65(5):485-495