:: DESCRIPTION
RNAmigos is a Graph Neural Network for predicting RNA small molecule ligands.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Oliver C, Mallet V, Gendron RS, Reinharz V, Hamilton WL, Moitessier N, Waldispühl J.
Augmented base pairing networks encode RNA-small molecule binding preferences.
Nucleic Acids Res. 2020 Aug 20;48(14):7690-7699. doi: 10.1093/nar/gkaa583. PMID: 32652015; PMCID: PMC7430648.
:: DESCRIPTION
EleKit allows to measure the complementarity in electrostatics between a docked small molecule and a protein receptor.
::DEVELOPER
Structural Bioinformatics Team
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2013 Oct 10;8(10):e75762. doi: 10.1371/journal.pone.0075762. eCollection 2013.
Electrostatic similarities between protein and small molecule ligands facilitate the design of protein-protein interaction inhibitors.
Voet A1, Berenger F, Zhang KY.
:: DESCRIPTION
ProBiS is a web server and a computer program for the detection of structurally similar protein binding sites and pairwise local structural alignment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W436-40. doi: 10.1093/nar/gkq479. Epub 2010 May 26.
ProBiS: a web server for detection of structurally similar protein binding sites.
Konc J1, Janezic D.
J Comput Chem. 2012 Oct 15;33(27):2199-203. doi: 10.1002/jcc.23048. Epub 2012 Jun 20.
Parallel-ProBiS: fast parallel algorithm for local structural comparison of protein structures and binding sites.
Konc J1, Depolli M, Trobec R, Rozman K, Janežič D.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W215-20. doi: 10.1093/nar/gku460. Epub 2014 May 26.
ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites.
Konc J1, Janežič D
:: DESCRIPTION
MotiveValidator is a platform for a set of applications designed to help you determine whether a residue or a ligand in a biomolecule or biomolecular complex is structurally complete and correctly annotated according to its models stored in the wwPDB Chemical Component Dictionary (wwPDB CCD).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes.
Vařeková RS, Jaiswal D, Sehnal D, Ionescu CM, Geidl S, Pravda L, Horský V, Wimmerová M, Koča J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W227-33. doi: 10.1093/nar/gku426.
:: DESCRIPTION
OpenGrowth is a research program which grows new ligands in proteins by connecting small organic fragments.
::DEVELOPER
The Shakhnovich Biophysics Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands.
Chéron N, Jasty N, Shakhnovich EI.
J Med Chem. 2015 Sep 23
:: DESCRIPTION
VSDMIP (Virtual Screening Data Management on an Integrated Platform) is divided in two parts: programs which actually do things (local packages) and program which translate those things to the database (cluster packages and cartridge).
::DEVELOPER
Unidad de Bioinformatica CBMSO
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface.
Cabrera áC, Gil-Redondo R, Perona A, Gago F, Morreale A.
J Comput Aided Mol Des. 2011 Sep;25(9):813-24. doi: 10.1007/s10822-011-9465-6.
:: DESCRIPTION
eBoxSize calculates an optimal box size for a query ligand in order to maximize the accuracy of molecular docking.
::DEVELOPER
Computational Systems Biology Group,
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Feinstein WP, Brylinski M.
Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets.
J Cheminform. 2015 May 15;7:18. doi: 10.1186/s13321-015-0067-5. PMID: 26082804; PMCID: PMC4468813.
:: DESCRIPTION
eMatchSite is a sequence order-independent algorithm for ligand binding site alignment and matching. It accurately identifies pairs of pockets that bind similar compounds even in proteins with different global structures. Furthermore, it tolerates structural distortions in protein models, thus experimentally solved structures are not required.
::DEVELOPER
Computational Systems Biology Group,
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.
Brylinski M.
PLoS Comput Biol. 2014 Sep 18;10(9):e1003829. doi: 10.1371/journal.pcbi.1003829.
:: DESCRIPTION
Twilight is a standalone script for analysis, visualization, and annotation of a pre-filtered set of protein/ligand complexes deposited with the PDB with ligand RSCC values that are below a threshold of 0.6.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Feb 1;69(Pt 2):195-200. doi: 10.1107/S1744309112044387.
Visualizing ligand molecules in Twilight electron density.
Weichenberger CX1, Pozharski E, Rupp B.
:: DESCRIPTION
LIGSIFT is a new computational method for the structural alignment of small molecules.
::DEVELOPER
Center for the Study of Systems Biology
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Oct 21. pii: btu692.
LIGSIFT: An open-source tool for ligand structural alignment and virtual screening.
Roy A, Skolnick J
