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| PubMed | |
| ISI Web of Knowledge | |
| Google Scholar | |
| PDB | Protein Data Bank |
| PDB_REDO | A databank with updated and optimised macromolecular X-ray diffraction structure models |
| Swiss-Model | Protein structure homology-modeling server |
| MODBASE | Database of Comparative Protein Structure Models |
| SCOP | Structural Classification of Proteins |
| CATH | Classification of protein domain structures |
| Binding MOAD | Subset of the PDB containing every high-quality example of ligand-protein binding. |
| Binding DB | Database of measured binding affinities |
| DrugBank | Database of detailed drug data and comprehensive drug target information |
| ChEMBL | Database of bioactive drug-like small molecules |
| Other EBI DBs | EBI Databases Index |
| DUD | A Directory of Useful Decoys |
| ZINC | A free database for Virtual Screening |
| CTD | Comparative Toxicogenomics Database |
| DSSTOX | Distributed Structure-Searchable Toxicity Database Network |
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| VMD | Visual Molecular Dynamics |
| YASARA View | Yet Another Scientific Artificial Reality Application |
| POV-Ray | Persistence of Vision Raytracer |
| PDBREPORT | Reports describing structural problems in PDB entries |
| PROCHECK | Verification of stereochemical quality of a protein structures |
| I-TASSER | Protein structure and function predictions |
| MODELLER | Comparative Protein Structure Modeling |
| PHYRE | Protein Fold Recognition |
| PMP | Protein Model Portal |
| Robetta | Full-chain Protein Structure Prediction Server |
| SitesModel | Collection of programs for the homology modelling of binding-sites based on known structures of related sites. |
| TMHMM | Prediction of transmembrane helices in proteins |
| NAMD | Molecular Dynamics Simulator |
| Gromacs | GROningen MAchine for Chemical Simulations |
| Desmond | High-speed molecular dynamics simulations |
| Wordom | Molecular simulation analysis and manipulation |
| TRAVIS | Trajectory Analyzer and Visualizer |
| Dynatraj |
| SURFNET | Program for the generation of protein surfaces and void regions |
| PASS | Program for tentative identification of drug interaction pockets from protein structure |
| PPI-Pred | Protein-Protein Interface Prediction |
| SHARP2 | Prediction of protein interaction sites on the surface of protein structures |
| FINDSITE | A threading-based method for ligand-binding site prediction |
| Q-SiteFinder | Ligand Binding Site Prediction |
| AutoDock | Multi-purpose automated docking tools |
| AutoDock Vina | High-throughput protein-ligand docking program |
| CDOCK | Protein-ligand docking with exhaustive conformational search |
| Haddock | High ambiguity driven protein-protein docking server |
| HEX | Online protein-protein docking using CPUs and GPUs |
| RosettaDock | Local protein-protein docking server |
| DOCK Blaster | Structure-based ligand discovery |
| DrugScore | Scoring Functions for Protein-Ligand Complexes |
| VSDMIP | Automated structure- and ligand-based virtual screening |
| ReverseScreen3D | Reverse virtual screening tool for protein target identification |
| SEA | Similarity ensemble approach tool for the construction of cross-target similarity maps |
| gCOMBINE | Structure-based Comparative Binding Energy Analysis |
| Open3DQSAR | Software for high-throughput chemometric analysis of molecular interaction fields |
| ToxCreate | Creates computational models to predict toxicity |
| T.E.S.T. | Toxicity Estimation Software Tool |
| CcpNmr | The Collaborative Computing Project for NMR |
| NMR Wiki | Open NMR Project |
| NMRPipe | Software system for processing, analysing, and exploiting NMR spectroscopic data |
| SBDS | Spectral Database for Organic Compounds |
| C-PAC | Analytical solution for time-resolved photoacoustic calorimetry data |
| CDK | Chemistry Development Kit |
| E-Dragon | Calculation of molecular descriptors |
| OpenBabel | The Open Source Chemistry Toolbox |
| Rosetta | Software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions |
| WHAT IF | A molecular modeling and drug design program |
| Weka | Machine learning algorithms for data mining tasks |
| R | Software environment for statistical computing and graphics |
| SVM Light | Implementation of Support Vector Machines |
| CLUTO | Data clustering software |
| KNIME | KoNstanz Information MinEr |
| Tcl | Tool Command Language |
| Perl | Perl Programming Language |
| Python | Python Programming Language |
| Foldit | Revolutionary computer game to unravel the secrets of protein folding |
| Alice | An educational software that teaches computer programming in a 3D environment |