:: DESCRIPTION
CH3Shift (CH3/methyl chemical shift predictor) is a method of calculating side-chain methyl chemical shifts from protein structures
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Biomol NMR. 2011 Aug;50(4):331-46. doi: 10.1007/s10858-011-9524-2. Epub 2011 Jul 12.
Structure-based prediction of methyl chemical shifts in proteins.
Sahakyan AB1, Vranken WF, Cavalli A, Vendruscolo M.
:: DESCRIPTION
Deduce is a now very old but still surprisingly effective correlation-based method of reconstructing molecular reaction networks from time-series data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PepBDB collected all the biological complex structures of peptide-mediated protein interactions with peptide lengths up to 50 residues in the Protein Data Bank.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
Wen Z, He J, Tao H, Huang SY.
PepBDB: a comprehensive structural database of biological peptide-protein interactions.
Bioinformatics. 2019 Jan 1;35(1):175-177. doi: 10.1093/bioinformatics/bty579. PMID: 29982280.
:: DESCRIPTION
parastructure is a perl script collection to run the population genetics software STRUCTURE in parallel on a cluster (beowulf type).
::DEVELOPER
Jacques Lagnel (lagnel@her.hcmr.gr)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
HemeNet, a support vector machine (SVM) based predictor, was developed to identify heme-binding residues by combining topological features with existing sequence and structural features.
::DEVELOPER
Machine Learning and Evolution Laboratory (MLEG)
:: SCREENSHOTS
n/a
:: REQUIREMENTS
NO
:: MORE INFORMATION
Citation:
PLoS One. 2011;6(10):e25560. doi: 10.1371/journal.pone.0025560. Epub 2011 Oct 3.
Computational prediction of heme-binding residues by exploiting residue interaction network.
Liu R1, Hu J.
:: DESCRIPTION
miRseqViewer is a highly interactive application that visualizes the sequence alignment, secondary structure and normalized read counts in synchronous multi-panel windows.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
miRseqViewer: Multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data.
Jang I, Chang H, Jun Y, Park S, Yang JO, Lee B, Kim W, Kim VN, Lee S.
Bioinformatics. 2014 Oct 15. pii: btu676.
:: DESCRIPTION
PCSS is a web server that allows a user to train new SVM models to make predictions for any protein that recognizes specific oligopeptide ligands.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2010 Jul 15;26(14):1714-22. doi: 10.1093/bioinformatics/btq267. Epub 2010 May 26.
Prediction of protease substrates using sequence and structure features.
Barkan DT1, Hostetter DR, Mahrus S, Pieper U, Wells JA, Craik CS, Sali A.
:: DESCRIPTION
ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments. As a Netscape plug-in , it can be embed into Web pages and controlled by JavaScript objects on the page. It has wide range of tools to manipulate and analyze sequences and structures by interactive control.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2003 Jan;19(1):165-6.
ModView, visualization of multiple protein sequences and structures.
Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A.
:: DESCRIPTION
PALES is a software for analysis of residual dipolar couplings. Its main component is the PALES (Prediction of ALignmEnt from Structure) simulation that predicts the magnitude and orientation of a sterically induced alignment tensor from a solute’s (protein/nucleic acid/oligosaccharide) three-dimensional shape.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
NMR: prediction of molecular alignment from structure using the PALES software.
Zweckstetter M.
Nat Protoc. 2008;3(4):679-90. doi: 10.1038/nprot.2008.36.
:: DESCRIPTION
Genome3D provides consensus structural annotations and 3D models for sequences from model organisms, including human.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.
Lewis TE,, et al.
Nucleic Acids Res. 2013 Jan;41(Database issue):D499-507. doi: 10.1093/nar/gks1266.
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.
Lewis TE and Sillitoe I, et al.
Nucleic Acids Res. 2013 Jan;41(Database issue):D499-507