Start Bioinformatics. Molecular docking. Directory of in silico Drug Design tools. SwissBioisostere - A database of molecular replacements for ligand design. GlobPlot 2.3 - Predictor of intrinsic protein disorder & globularity. PHYRE2 Protein Fold Recognition Server. Molecular docking. NIH MBI Laboratory for Structural Genomics and Proteomics.
The UCLA-DOE Structure Evaluation server is a tool designed to help in the refinement of crystallographic structures.
It will provide you with a visual analysis of the quality of a putative crystal structure for a protein. Verify3D expects this crystal structure to be submitted in PDB format. Please note that Verify3D works best on proteins with at least 100 residues. To submit a crystal structure for analysis, simply select it with the file dialog which is activated by clicking on the Browse button below, then click the Send File button. Obtain your own standalone copy of Profile Search/Environments program/Verify 3D References: [Bowie et al., 1991; Luethy et al., 1992].
Protein Model Portal - PSI SBKB. Protein Model Portal - PSI SBKB. 3D-JIGSAW Protein Comparative Modelling Server. Robetta: full-chain protein structure prediction server. ModWeb. DrugBank. HADDOCK webserver. Nouvel onglet. Molecular Docking Server - Ligand Protein Docking & Molecular Modeling. You can start single molecular docking calculations or high-throughput virtual screening with few clicks carry out focused docking to a known binding site carry out blind docking experiments to determine possible binding site(s) calculate inhibition constants, binding geometry, secondary interactions & much more prepare publication quality figures and a method section for your reports automatically organize proteins and ligands into user-defined libraries carry out molecular docking on-line STEP 1 – Preparation of ligands Draw your ligands using a Java applet, upload a single ligand file or multiple ligands.
Draw chemical structures by MarvinSketch, a Java based program with a constantly growing list of editing features and a number of templates to make molecule drawing simpler. Upload a ligand in MDL MOL, SYBYL MOL2, PDB, HYPERCHEM HIN or SMILES format. STEP 2 – Preparation of proteins STEP 3 – Setup ligand protein docking calculations Select a protein and a ligand from your library. Orientations of Proteins in Membranes (OPM) database. ETH - EPR - Software. An open-source program for visualization, inspection, generation, and improvement of models of proteins and protein assemblies based on restraints from multiple experimental techniques.
Version 2013 introduces an estimate of model quality for structural transitions, adapted rotamer libraries, and systematic and automated tests of rotamer libraries against experimental data. Help files for modeling of structural transitions were improved. Download MMM 2013 (104 Mb). Download User manual only (3.0 Mb) DeerAnalysis2013 A program for extracting distance distributions from dead-time free pulsed electron electron double resonance (DEER, PELDOR) data with Matlab. Download DeerAnalysis2013 (106 Mb). An open-source program for visualization, inspection, and improvement of models of proteins and protein assemblies based on restraints from multiple experimental techniques.
Download MMM 2011.2 (90 Mb) Download the newest User manual only (3.0 Mb) Disprot - Database of Protein Disorder. LigPlot+ home page. Protein Modeling Tool. Triacylglycerol Lipase (EC 3.1.1.3 ) Database. PMDB - Protein Model DataBase. Applications — Site. 3D protein model prediction.