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URLs Virtual screening - Protein-ligand interactions, some aspects of chemical space Comments
Platinum A database of experimentally measured effects of mutations on structurally defined protein-ligand complexes (around 1000 mutations in 2014) online
Rocker Open source, easy-to-use tool for AUC and enrichment calculations and ROC curve visualization online
ATT2 An Efficient and Versatile Tool for Lead Structure Generation and Optimization (ATT2) online
JADOPPT Java based AutoDock Preparing and Processing Tool online
RADER RApid DEcoy Retriever to facilitate decoy based assessment of virtual screening online
CSM-lig A server for assessing and comparing protein–small molecule affinities (predict binding affinities) (scoring) online
Vinardo A Scoring Function Based on Autodock Vina Improves Scoring, Docking, and Virtual Screening (2016) standalone
PLIff Protein-Ligand-Informatics force field (PLIff): towards a fully knowledge driven “force field” for biomolecular interactions (PLI 2016) standalone
ePlatton According to the 2D structure similarity, ligands are classified into different ligand clusters, which can considerably reduce the redundancy of the ligand range of targets. ePlatton relates the ligand clusters to their targets and also integrates the information of disease, pathway, drug adverse reaction (DAR) and approved drug online
DockAccessor An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design standalone
MANORAA Mapping Analogous Nuclei Onto Residue And Affinity for identifying protein–ligand fragment interaction, pathways and SNPs online
MEPSA Minimum energy pathway analysis for energy landscapes standalone
Bio-AIMS Bio-AIMS Collection of Chemoinformatics Web Tools based on Molecular Graph Information and Artificial Intelligence Models. Six tools predict protein activity, two models evaluate drug - protein target interactions and the other three calculate protein - protein interactions. The molecular graph descriptor-based Machine Learning models could be useful tools for in silico screening of new peptides/proteins (2015) online
MolBridge A program for finding non-bonded interactions in small molecule and biomolecule structures online and standalone
Rchemcpp A web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map online
Similarity Mapplet Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces (2015) online
Halogen Evaluating the Potential of Halogen Bonding in Molecular Design. Scoring and visualization of halogen bonds toward backbone carbonyls should be available via a Web interface standalone
Cyscore Benchmark tests show that this model significantly improves the protein-ligand scoring and Cyscore outperforms a variety of well established scoring functions using PDBbind benchmark sets for binding affinity correlation and ranking tests standalone
cholmine Determinants and Prediction of Cholesterol and Cholate Binding Across Nonhomologous Protein Structures online with registration
Chemo tools The NCATS Informatics group. Automated R-group analysis, Fragment activity profiler, library synthesizer, tautomer generator, standardizer...Scaffold hopper, molecular framework, scaffold activity, Tox21 chemical browser, Siphony standalone
PreDDICTA Predict DNA-Drug Interaction strength by Computing deltaTm and Affinity of binding online
VAMMPIRE-LORD A Web Server for Straightforward Lead Optimization Using Matched Molecular Pairs online
RNA tool LigandRNA: computational predictor of RNA–ligand interactions online
BRICS Modelling of chemical space based on prominent chemical motifs of known inhibitors and commercially available compounds standalone
Polyphony Superposition independent methods for ensemble-based drug discovery. Currently, methods capable of the analysis of ensembles of crystal structures and MD trajectories are limited and usually rely upon least squares superposition of coordinates. New methodologies are described and validated for the superimposition independent conformational analysis of large collections of structures or simulation snapshots of the same protein. The methodologies are encoded in a Python package standalone
sc-PDB-Frag A database of protein-bound fragments that assists in selecting truely bioisosteric scaffolds (bioisostere) online
Protoss A holistic approach to predict tautomers and protonation states in protein-ligand complexes online
PHENIX Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package standalone
NAOMI NAOMI is a command-line tool for the consistent conversion of common chemical file formats (SDF, SMILES, MOL2) standalone
RosettaBackrub Flexible backbone protein structure modeling and design server. Can be used for Point mutation, Backbone ensemble (creates near-native structural ensembles), Sequence tolerance (predicts sequences tolerated for proteins and protein-protein interfaces using flexible backbone design methods. Example applications are the generation of sequence libraries for experimental screening and prediction of protein or peptide interaction specificity) online
3DFIT 3D Fragment Consortium: collection of chemically diverse molecules with a particular focus on fragments that incorporate 3D structure online
In Silico Molecules Open Source Drug Design and In Silico Molecules. An open access database of in-silico compounds from which New Potent Chemical Entities can be developed as potential new molecules of different categories for the treatment of various kinds of diseases online
e-LEA3D e-Drug3D Chemical content of the collection of commercial fragments (privileged structures) extracted from the FDA approved drugs online
LPCCSU Analysis of interatomic Contacts in Ligand-Protein complexes online
RF-Score Predicting protein–ligand binding affinity standalone
FragVLib FragVLib a free database mining software for generating Fragment-based Virtual Library using pocket similarity search of ligand-receptor complexes. A free software which is developed as a tool for performing similarity search across database(s) of ligand-receptor complexes for identifying binding pockets which are similar to that of a target receptor standalone
MQN-Mapplet Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13



CHpredict The CHpredict server predict two types of interactions: C-H...O and C-H...pi interactions online
WaterDock A fast and accurate method that predicts the location of water molecules in protein structures. The method's simplicity is the key to its speed; water molecules are docked into a structure using AutoDock Vina, low scoring sites are removed and the rest are clustered. The centroids of the clusters are the predicted water sites standalone
DiSCuS An open platform for (not only) virtual screening results management standalone
GOMoDo GPCR Online Modeling and Docking provides a single web interface and pipeline to model GPCRs and to dock molecules into the model online
SwissBioisostere Chemistry tool database and online
SSCAN Canonical Signatures: Canonical signatures are representations of the local structure of molecules online
MolClass Rapid Molecule Classification Based on Structure and Activity: REST service is available based on the OpenTox API 1.2 standalone
PROFEAT Protein Feature Server for computing physicochemical properties of proteins and peptides from their primary sequences Protein Feature Server - SVM, online
ProtParam  A tool which allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY) for SVM - protein parameter, online
VSDMIP  A platform for virtual screening (VS) of chemical libraries, integrated within a MySQL relational database. Virtual screening, structure-based screening. See also cdock pipelines, standalone
KNIME Workflow data flows, standalone
Taverna The Taverna project aims to provide a language and software tools to facilitate easy use of workflow and distributed compute technology within the eScience community data flows, standalone
XBaya  A Graphical Workflow Composer for Web Services Data flows, standalone
SARANEA  A freely available program to mine structure-activity and structure-selectivity relationship information in compound data sets, activity cliff. Bajorath et al. J. Chem. Inf. Model., 2010. Also several compound collections for hERG, proteases... Chemoinformatics, standalone
Pubchem similarity Compare ligand using a substructure key-based 2D Tanimoto similarity via the PubChem score matrix web service online
PubChem subsets Maximum unbiased validation (MUV) data sets for virtual screening based on PubChem bioactivity data Datasets