Binding Site Prediction and Docking
The interaction between proteins and other molecules is fundamental to all biological functions. In this section we include tools that can assist in prediction of interaction sites on protein surface and tools for predicting the structure of the intermolecular complex formed between two or more molecules (docking).
| open in new windowCASTp | Automatic Identification of pockets and cavities in proteins structure, and quantitation of their volumes using Delaunay triangulation. Available also as PyMOL plugin |
|---|---|
| open in new windowPocket-Finder | Automatic identification of pockets and cavities in proteins structure, and quantitation of their volumes. |
| open in new windowPocketPicker | Grid-based technique for the analysis of protein pockets. PocketPicker available as a plugin for PyMOL |
| open in new windowConSurf | Identification of functional regions in proteins by surface-mapping of phylogenetic information |
|---|---|
| open in new windowCRESCENDO | Identification protein interaction sites. It uses sequence conservation patterns in homologous proteins to distinguish between residues that are conserved due to structural restraints from those due to functional restraints. |
| Ligand Binding Sites | |
| open in new window3DLigandSite | The server utilizes protein-structure prediction to provide structural models of the binding site. Ligands bound to structures are superimposed onto the model and use to predict the binding site. |
| open in new windowFINDSITE | A threading-based method for ligand-binding site prediction and functional annotation based on binding-site similarity across superimposed groups of threading templates. |
| open in new windowLIGSITEcsc | Prediction of binding site by pocket identification using the Connolly surface and degree of conservation |
| open in new windowmetaPocket | A meta server for ligand-binding site prediction. metaPocket use LIGSITEcsc, PASS, Q-SiteFinder and SURFNET |
| open in new windowcons-PPISP | A consensus neural network method for predicting protein-protein interaction sites |
|---|---|
| open in new windowHOMCOS | A server to predict interacting protein pairs and interacting sites by homology modeling of complex structures |
| open in new windowHotPOINT | Prediction of protein interfaces using an empirical model |
| open in new windowISIS | Prediction of interaction hotspots from sequence |
| open in new windowKFC server | Automated decision-tree approach to predicting protein-protein interaction hot spots |
| open in new windowmeta-PPISP | A meta server for predicting protein-protein interaction sites. meta-PPISP is built on three individual web servers: cons-PPISP, PINUP, and Promate |
| open in new windowODA | Identification of optimal surface patches with the lowest docking desolvation energy values |
| open in new windowPINUP | Protein binding site prediction with an empirical scoring function |
open in new windowCHED  |
Web server for predicting soft metal binding sites in proteins |
|---|---|
| open in new windowDBD-Hunter | A knowledge-based method for the prediction of DNA-protein interactions |
| open in new windowDISPLAR | Given the structure of a protein known to bind DNA, the method predicts residues that contact DNA using neural network method |
| open in new windowiDBPs | Predicts DNA binding proteins for proteins with known 3D structure. |
| open in new windowPFplus | A tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces. |
Search Method |
Flexibility |
Scoring Function |
Cost | ||
|---|---|---|---|---|---|
| open in new windowAutoDock | Stochastic (GA) | Flexible ligand and partially flexible target | AUTODOCK(empirical) | Free |  |
| open in new windowArgusLab | Systematic |
Flexible ligand | X-Score based (empirical) | Free | |
| open in new windowDOCK | Systematic (IC) | Flexible ligand | DOCK 3.5 (force field) | Free for academics | |
| open in new windoweHITS | Systematic (RBD of fragments followed by reconstruction) | Flexible ligand and partially flexible target | HiTS_Score (empirical) | Free for academics | |
| open in new windowFlexX | Systematic (IC) | Flexible ligand | FlexX SF (empirical) | Commercial | |
| open in new windowFLIPDock | Stochastic (GA) | Flexible ligand and flexible target | AUTODOCK (empirical) | Free for academics | |
| open in new windowFRED | Systematic (RBD) | Flexible ligand | ChemScore, PLP, ScreenScore, ChemGauss (empirical/consensus) | Free for non-commercial projects | |
| open in new windowGOLD | Stochastic (GA) | Flexible ligand and partially flexible target | GoldScore, ChemScore (empirical), ASP (knowledge based) | Commercial | |
| open in new windowICM | Stochastic (MC) | Flexible ligand and partially flexible target | ICM SF (empirical) | Commercial | |
| open in new windowParDOCK | Stochastic (MC) | Rigid | BAPPL (empirical) | open in new windowWeb Server | |
| open in new windowPLANTS | Stochastic (ACO) | Flexible ligand and partially flexible target | CHEMPLP, PLP (empirical) |
Free for academics | |
| open in new windowSurflex | Systematic (IC/MA) | Flexible ligand | Hammerhead based (empirical) | Commercial | |
| open in new windowBAPPL | computing binding free energy of a non-metallo protein-ligand complex using an all atom energy based empirical scoring function | ||||
|---|---|---|---|---|---|
| open in new windowBAPPL-Z | Binding affinity prediction of protein-ligand complex containing Zinc | ||||
| open in new windowDrugScore | Knowledge-based scoring functions. DrugScore enables you to score protein-ligand complexes of your interest and to visualize the per-atom score contributions. | ||||
| open in new windowFoldX | Protein-protein binding energy calculations | ||||
| open in new windowgCOMBINE | A java-written graphical user interface for performing comparative binding energy analysis | ||||
| open in new windowGFscore | A general non-linear consensus scoring function for high-throughput docking | ||||
| open in new windowPEARLS | Computing small molecule ligand-protein, ligand-nucleic acid, protein-nucleic acid and ligand-protein-nucleic acid interaction energies | open in new windowPreDDICTA | Calculates the Drug-DNA interaction energy | ||
| Compound Databases for Virtual Screening | |||||
| open in new windowZINC | Free database of commercially-available compounds for virtual screening | ||||
| Ligand Entrance and Exit Channels | |
|---|---|
| open in new windowSLITHER | A web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating across membrane transporters |
| Search Algorithm | Scoring Parameters | Re-scoring, Ranking, Filtering and Refinement | Cost | ||
|---|---|---|---|---|---|
| open in new window3D-Dock Suite | Global rigid search: FFT | Shape complementarity and electrostatics | Re-scoring and clustering. Refinement of interface side-chains | Free | |
| open in new window3D-Garden | Global rigid search in ensamble | Shape complementarity and Lennard–Jones potential |
Side chain and backbone dihedral refinement | ||
| open in new windowDOT | Global rigid search: FFT | Shape complementarity, electrostatics and VDW | None | Free for academics | |
| open in new windowEscher NG | Global rigid search | Shape complementarity, hydrogen bonds and electrostatic | None | Free |
|
| Integrated in open in new windowVEGA | |||||
| open in new windowGRAMM | Global rigid search: FFT. smooth protein surface representation for soft docking | Shape complementarity and Lennard-Jones potential | Clustering of conformations | Free | |
| open in new windowGRAMM-X | Global rigid search: FFT. smooth protein surface representation for soft docking | Shape complementarity and Lennard-Jones potential | minimization and re-scoring with multiple filters | open in new windowWeb Server | |
| open in new windowHEX | Global rigid search: Fourier correlation of spherical harmonics | Shape complementarity | None | Web Server | |
| source code is available for open in new windowdownload | |||||
| open in new windowHADDOCK | Global rigid search | Electrostatic ,VDW and desolvation energy terms | MD simulated annealing refinement . Filtering based on external data. clustering and re-ranking | Web server | |
| source code is available for open in new windowdownload | |||||
| ICM | Global rigid search: Monte Carlo | Empirical scoring function | Clustering and selection of conformations. Refinement of interface side-chains and re-scoring | Commercial | |
| open in new windowMolFit |
Global rigid search: FFT | Shape complementarity | Clustering of good solutions, filtering using a priori information and small, local rigid rotations around selected conformations | Free | open in new windowPatchDock | Global rigid search | Shape complementarity and atomic desolvation energy | Clustering of conformations |
| source code is available for download | |||||
| open in new windowPyDock | Global rigid search: FFT | Shape complementarity | rescoring by binding electrostatics and desolvation energy | open in new windowWeb Server | |
| open in new windowRosettaDock | Local rigid search: Monte Carlo with low and high resolution structure representation levels | Different scoring parameters for the different resolutions | open in new windowWeb Server | ||
| source code is available by license from open in new windowRosettaCommons. | |||||
| open in new windowZDOCK | Global rigid search: FFT | Shape complementarity, desolvation energy, and electrostatics. | Energy minimization and re-scoring | Free for academics | |
| Post Docking Re-scoring, Ranking, Filtering and Refinement | |||||
| open in new windowFireDock | Refinement and re-scoring of rigid-body protein-protein docking solutions | ||||
| open in new windowFunHunt | Classifier of correct protein-protein complex orientations | ||||
| RosettaDock | Local docking. Useful for refining top-ranked models from global searches by other docking methods. | ||||