Databases

Zinc Database, ChEMBL, CoCoCo, Protein DataBank (PDB), Binding MOAD (Mother Of All Database), Ligand Protein DataBase (LPDB), TTD, STITCH,SMPDB, ...
Chemical structure representations

ChemDraw, MarvinSketch, ACD/ChemSketch, ChemWriter, jsMolEditor, Marvin molecule editor and viewer, UCSF Chimera, Pymol, Swiss-PDB Viewer / DeepView, Daylight SMILES, InChI, Tripos Mol2, OpenBabel, LigPrep, Corina, PoseView, DS Visualizer, EBabel, Corina online demo, Chemical Identifier Resolver, ChemMobi, ...
Molecular Modeling

CHARMM, GROMACS, Amber, SwissParam, Dundee PRODRG2 Server, PDB2PQR Server, SwissSideChain, ...
Homology Modeling

Modeller, I-TASSER, LOMETS, SWISS-MODEL, SWISS-MODEL Repository, ModBase, ...

MED-SuMo, CAVER, FINDSITE, scPDB, CASTp, Pocketome, 3DLigandSite, metaPocket, PocketQuery, ...
Docking

Autodock, DOCK, GOLD, SwissDock, DockingServer, Blaster, COPICAT, ...

CoLibri, Corina, Pharmer, Blaster, FINDSITE-LHM, AnchorQuery, ...

GANDI, LUDI, SPROUT, Glide Fragment Library, eLEA3D, 3DLigandSite, PASS, ...
Binding free energy estimation

X-score, eHITS_Score, DrugScoreONLINE, BAPPL server, BAPPL-Z server, ...

QSAR

cQSAR, clogP, ClogP/CMR, MOLE db, ChemDB/Datasets, Datasets from the Milano Chemometrics and QSAR Research Group, OCHEM, MolInfo, E-Dragon, ...
ADME Toxicity

QikProp, q-ADME, q-TOX, ALOGPS, OSIRIS Property Explorer, ToxPredict, TOXNET, Leadscope Toxicity Database, Cloe Knowledge, ...
BioDrugScreen. Computational drug design and discovery resource and server. The portal contains the DOPIN (Docked Proteome Interaction Network) database constituted by millions of pre-docked and pre-scored complexes from thousands of targets from the human proteome and thousands of drug-like small molecules from the NCI diversity set and other sources. The portal is also a server that can be used to (i) customize scoring functions and apply them to rank molecules and targets in DOPIN; (ii) dock against pre-processed targets of the PDB; and (iii) search for off-targets. Maintained by the laboratory of Samy Meroueh at the Center for Computational Biology and Bioinformatics at the Indiana University School of Medicine. PHYSPROP. The Physical Properties Database (PHYSPROP) contains chemical structures, names, and physical properties for over 41,000 chemicals. Physical properties are collected from a wide variety of sources, and include experimental, extrapolated, and estimated values for melting point, boiling point, water solubility, octanol-water partition coefficient, vapor pressure, pKa, Henry's Law Constant, and OH rate constant in the atmosphere. Maintained by SRC. SEA. (Similarity ensemble approach) relates proteins based on the set-wise chemical similarity among their ligands. It can be used to rapidly search large compound databases and to build cross-target similarity maps. Provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). MOLFEAT. Web service to compute molecular fingerprints and molecular descriptors of molecules from their 3D structures, and for computing activity of compounds of specific chemical types against selected targets based on published Quantitative Structure-Activity Relationship (QSAR) models. Currently covers 1,114 fingerprints, 3,977 molecular descriptors, and 23 QSAR models for 16 chemical types against 14 targets. Maintained by the University of Singapore. SPORES. (Structure PrOtonation and REcognition System). Structure recognition tool for automated protein and ligand preparation. SPORES generates connectivity, hybridisation, atom and bond types from the coordinates of the molecule`s heavy atoms and hydrogen atoms to the structure. The protonation can either be done by just adding missing hydrogen atoms or as a complete reprotonation. SPORES is able to generate different protonation states, tautomers and stereoisomers for a given structure. Developed by the Konstanz university. PLANTS. (Protein-Ligand ANT System). Docking algorithm based on a class of stochastic optimization algorithms called ant colony optimization (ACO). In the case of protein-ligand docking, an artificial ant colony is employed to find a minimum energy conformation of the ligand in the binding site. These ants are used to mimic the behavior of real ants and mark low energy ligand conformations with pheromone trails. The artificial pheromone trail information is modified in subsequent iterations to generate low energy conformations with a higher probability. Developed by the Konstanz university. Zodiac. Free open source molecular modelling suite for computation, analysis and display of molecular data. It features state-of-the-art tools for managing molecular databases, run molecular docking experiments, compute raytraced images, etc... Developed by Zeden. Zeden. Free open source molecular editor, for Windows and Mac OSX. Developed by Zeden.

QUARK. Internet service for ab initio protein folding and protein structure prediction, which aims to construct the correct protein 3D model from amino acid sequence only. QUARK models are built from small fragments (1-20 residues long) by replica-exchange Monte Carlo simulation under the guide of an atomic-level knowledge-based force field. QUARK was ranked as the No 1 server in Free-modeling (FM) in CASP9. Since no global template information is used in QUARK simulation, the server is suitable for proteins which are considered without homologous templates. Provided by the University of Michigan. CABS. Versatile reduced representation tool for molecular modeling, including: de novo folding of small proteins, comparative modeling (especially in cases of poor templates) and structure prediction based on sparse experimental data. Developed by the Warsaw University. PEP-FOLD. De novo approach aimed at predicting peptide structures from amino acid sequences. This method, based on structural alphabet SA letters to describe the conformations of four consecutive residues, couples the predicted series of SA letters to a greedy algorithm and a coarse-grained force field. Developed by the University of Paris Diderot. SiteComp. Web server providing three major types of analysis based on molecular interaction fields: binding site comparison, binding site decomposition and multi-probe characterization. Maintained by the Sanchez lab, at the Mount Sinai School of Medicine, NY, USA. DockoMatic. GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions. ParaDockS. (Parallel Docking Suite). Free, open source program, for docking small, drug-like molecules to a rigid receptor employing either the knowledge-based potential PMF04 or the empirical energy function p-Score. BDT. Graphic front-end application which control the conditions of AutoGrid and AutoDock runs. Maintained by the Universitat Rovira i Virgili, GFscore. Web server to discriminate true negatives from false negatives in a dataset of diverse chemical compounds using a consensus scoring in a Non-Linear Neural Network manner. The global scoring function is a combination of the five scoring functions found in the Cscore package from Tripos Inc. GLIDA. GPCR-Ligand Database. Provides information on both GPCRs and their known ligands. Enterable either by GPCR search or ligand search. Maintained by the PharmacoInformatics Laboratory, Kyoto University. Ki Database. Provides information on the abilities of drugs to interact with an expanding number of molecular targets. The Ki database serves as a data warehouse for published and internally-derived Ki, or affinity, values for a large number of drugs and drug candidates at an expanding number of G-protein coupled receptors, ion channels, transporters and enzymes. Currently 55472 Ki values. Maintained by the NIMH Psychoactive Drug Screening Program. AURAmol. Web service taking a candidate 2D or 3D molecular shape and use it to search for similarly shaped molecules in large databases. Provided by the University of York. MultiBind. (Multiple Alignment of Protein Binding Sites). Prediction tool for protein binding sites. Users input a set of protein-small molecule complexes and MultiBind predicts the common physio-chemical patterns responsible for protein binding. Exists as a standalone program. Provided by the structural Bioinformatics group at Tel-Aviv University. FOBIA. Folding by hierarchical assembly. Provided by the structural Bioinformatics group at Tel-Aviv University. MATCH. (Multipurpose Atom-Typer for CHARMM). Toolset of program libraries collectively titled multipurpose atom-typer for CHARMM (MATCH) for the automated assignment of atom types and force field paramters for molecular mechanics simulation of organic molecules. Developed by the Brooks lab, Michigan university. QuteMol. Open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins. Developed by the Visual Computing Lab at ISTI-CNR, Italy. MolProbity. Web service for all-atom structure validation for macromolecular crystallography. Maintained by the Richardson Lab, Duke University. ProBis. Web server for detection of structurally similar binding sites. Maintained by the National Institute of Chemistry, Ljubljana, Slovenia.

Dehydron. A dehydron calculator plugin for PyMOL. This plugin calculates dehydrons and display them onto the protein structure. COPICAT. (COmprehensive Predictor of Interactions between Chemical compounds And Target proteins). System for predicting interactions between chemical compounds and proteins by using Support Vector Machine (SVM). COPICAT realizes comprehensive prediction of protein-chemical interactions by utilizing very general, or the most easily available, data i.e. amino acid sequences and chemical structures. Maintained by the Sakakibara Lab., Dept. Biosciences and Informatics, Keio University. CSAR. (Community Structure-Activity Resource). Resource for Docking and Scoring Development. Provides experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes. Cloe Knowledge. Open Access ADME/PK Database for a range of marketed drugs. Maintained by Cyprotex. DART. (Drug Adverse Reaction Target). A database for facilitating the search for drug adverse reaction target. It contains information about known drug adverse rection targets, functions and properties. Associated references are also included. Maintained by the University of Singapore. Molecule Viewer 3D. Opens most common 3D molecule file formats saved on a SD card or found in a library of 243 included molecules. For Android. Atomdroid. Free computational chemistry tool. It can be used as a molecular viewer/builder and contains local optimization and Monte Carlo simulation features. For Android. PubChem Mobile. Free application to search PubChem databases using chemical names, synonyms, and keywords. For Android. MolPad. Free chemical structure drawing application. It can draw structures from scratch or load them from ChemSpider and modify them. Structures can be emailed in Molfile format. For Android. DCE ChemPad. Free application to draw chemical structures and calculate molecular weight, molecular formula and to send the molfile. It shows the capabilities of the Dendro Chemical Editor control for Android to build chemistry-aware mobile applications. For Android. Jmol Molecular Visualization. Free Jmol for Android tablets. GLmol. Free and open source 3D molecular viewer based on WebGL and Javascript. GLmol runs on newer versions of Firefox, Chrome, Safari or Opera. Internet Explorer is not supported. GLmol also runs on Sony Ericsson's Android devices which support WebGL and WebGL enabled safari in iOS. Atomdroid. Free computational chemistry tool. It can be used as a molecular viewer/builder and contains local optimization and Monte Carlo simulation features. For Android. Atom 3D. Free application to visualize molecules and crystal structures in 3D using the touchscreen to rotate and zoom. Includes 19 sample structures. Supports XYZ files and some protein data bank (PDB) files. For Android. PDB View 3D. Application for molecular graphics visualization from PDB files. For Android.