:: DESCRIPTION
OpenAstexViewer is a Java molecular graphics program that assists in structure based drug design. It can be used as an Applet in a web page or as a desktop application.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hartshorn MJ.
AstexViewer: a visualisation aid for structure-based drug design.
J Comput Aided Mol Des. 2002 Dec;16(12):871-81.
:: DESCRIPTION
epitope3D is a novel scalable machine learning method capable of accurately identifying conformational epitopes trained and evaluated on the largest curated epitope data set to date.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
da Silva BM, Myung Y, Ascher DB, Pires DEV.
epitope3D: a machine learning method for conformational B-cell epitope prediction.
Brief Bioinform. 2021 Oct 21:bbab423. doi: 10.1093/bib/bbab423. Epub ahead of print. PMID: 34676398.
:: DESCRIPTION
K-Fold is a tool for the automatic prediction of the protein folding kinetic order and rate. The tool is based on a support vector machine (SVM) that was trained on a data set of 63 proteins, whose 3D structure and folding mechanism are known from experiments already described in the literature.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2007 Feb 1;23(3):385-6. Epub 2006 Nov 30.
K-Fold: a tool for the prediction of the protein folding kinetic order and rate.
Capriotti E, Casadio R.
:: DESCRIPTION
Wordom is a (simple) command line utility conceived to spare the user some time in manipulating and converting dcd, xtc, pdb, crd and xyz files. Wordom is also a versatile program for a broad range of molecular structure and dynamics analysis.
::DEVELOPER
the Fanelli Lab at the University of Modena and Reggio Emilia (IT)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
M. Seeber, A. Felline, F. Raimondi, S. Muff, Ran Friedman, F. Rao, A. Caflisch and F. Fanelli;
Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces;
J. Comp. Chem., 2011, 6(32):1183-1194; doi:10.1002/jcc.21688
:: DESCRIPTION
MSPocket is an orientation independent program for the detection and graphical analysis of protein surface pockets.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhu H, Pisabarro MT.
MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets.
Bioinformatics. 2011 Feb 1;27(3):351-8.
:: DESCRIPTION
Pentacle is an advanced software tool for obtaining alignment-independent 3D quantitative structure-activity relationships. The program starts from a set of structures, computing highly relevant 3D maps of interaction energies between the molecule and chemical probes (GRID based Molecular Interaction Fields, or MIFs). Pentacle automatically encodes these maps into GRID Independent Descriptors (GRIND and GRIND2 descriptors), which are independent of the alignment of the series, thus bypassing one of the most time-consuming aspects of traditional 3D QSAR.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Chem Inf Model. 2009 Sep;49(9):2129-38.
Suitability of GRIND-based principal properties for the description of molecular similarity and ligand-based virtual screening.
Durán A, Zamora I, Pastor M.
:: DESCRIPTION
The program Ringer detects molecular motions by automatic electron density sampling. The aim of Ringer is to go beyond static structural snapshots of proteins by uncovering structural ensembles in X-ray electron density. This information can reveal not only which parts of proteins are flexible and which part are rigid, but it also can define alternate conformations that may be important for function. Alternate conformations of binding sites also may afford additional targets for drug design.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lang et al.
Automated electron-density sampling reveals widespread conformational polymorphism in proteins.
Protein Sci.: 2010, 19(7);1420-31.
:: DESCRIPTION
ANOLEA (Atomic Non-Local Environment Assessment) is a server to assess the quality of a three – dimensional protein structure. It uses a statistical potential at the atomic level and gives an energy profile as ouput. Also, the user can choose to have a molecular graphical output representation of the energy profile.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Proc Int Conf Intell Syst Mol Biol. 1997;5:187-90.
ANOLEA: a www server to assess protein structures.
Melo F, Devos D, Depiereux E, Feytmans E.
:: DESCRIPTION
SEED is a program for docking libraries of fragments with solvation energy evaluation.The docking approach implemented in the program SEED determines optimal positions and orientations of small-to-medium-sized molecular fragments in the binding site of a rigid protein (hereafter also referred to as receptor) and ranks them according to their binding energy.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Majeux N, Scarsi M, Caflisch A
Efficient electrostatic solvation model for protein-fragment docking.
Proteins: Struct. Funct. Genet 42, 256-268, 2001
:: DESCRIPTION
ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes.
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:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Comput Aided Mol Des. 2010 Feb;24(2):91-105. doi: 10.1007/s10822-009-9317-9. Epub 2010 Jan 30.
Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function.
Garden DP, Zhorov BS.
