#dockingtools
#structurebioinformatics
Please find the list of Docking Softwares
Autodock. Free open source EA based docking software. Flexible ligand. Flexible protein side chains. Maintained by the Molecular Graphics Laboratory, The Scripps Research Institute, la Jolla.
DOCK. Anchor-and-Grow based docking program. Free for academic usage. Flexible ligand. Flexible protein. Maintained by the Soichet group at the UCSF.
GOLD. GA based docking program. Flexible ligand. Partial flexibility for protein. Product from a collaboration between the university of Sheffield, GlaxoSmithKline plc and CCDC.
SCIGRESS. Desktop/server molecular modeling software suite employing linear scaling semiempirical quantum methods for protein optimization and ligand docking. Developed and distributed by Fujitsu, Ltd.
GlamDock. Docking program based on a Monte-Carlo with minimization (basin hopping) search in a hybrid interaction matching / internal coordinate search space. Part of the Chil2 suite. Open for general research.
FlexAID. A small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function. The pairwise energy parameters were derived from a large dataset of true positive poses and negative decoys from the PDBbind database through an iterative process using Monte Carlo simulations. Precompiled Linux, MacOS and Windows versions are made available by the University of Sherbrooke, Canada.
GEMDOCK. Generic Evolutionary Method for molecular DOCKing. Program for computing a ligand conformation and orientation relative to the active site of target protein
iGEMDOCK. Graphic environment for the docking, virtual screening, and post-screening analysis. Free for non commercial researches. For Windows and Linux.
HomDock. Progam for similarity-based docking, based on a combination of the ligand based GMA molecular alignment tool and the docking tool GlamDock. Part of the Chil2 suite. Open for general research.
ICM. Docking program based on pseudo-Brownian sampling and local minimization. Ligand and protein flexible. Provided by MolSoft.
FlexX, Flex-Ensemble (FlexE). Incremental build based docking program. Flexible ligand. Protein flexibility through ensemble of protein structure. Provided by BioSolveIT.
Fleksy. Program for flexible and induced fit docking using receptor ensemble (constructed using backbone-dependent rotamer library) to describe protein flexibility. Provided by the Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen.
FITTED. (Flexibility Induced Through Targeted Evolutionary Description). Suite of programs to dock flexible ligands into flexible proteins. This software relies on a genetic algorithm to account for flexibility of the two molecules and location of water molecules, and on a novel application of a switching function to retain or displace water molecules and to form potential covalent bonds (covalent docking) with the protein side-chains. Part of the Molecular FORECASTER package and FITTED Suite. Free for an academic site license (excluding cluster).
VLifeDock. Multiple approaches for protein - ligand docking. Provides three docking approches: Grid based docking, GA docking and VLife's own GRIP docking program. Several scoring functions can be used: PLP score, XCscore and Steric + Electrostatic score. Available for Linux and Windows. Provided by VLife.
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.
DAIM-SEED-FFLD. Free open source fragment-based docking suite. The docking is realized in three steps. DAIM (Decomposition And Identification of Molecules) decomposes the molecules into molecular fragments that are docked using SEED (Program for docking libraries of fragments with solvation energy evaluation). Finally, the molecules are reconstructed ''in situ'' from the docked fragments using the FFLD program (Program for fragment-based flexible ligand docking). Deve
#structurebioinformatics
Please find the list of Docking Softwares
Autodock. Free open source EA based docking software. Flexible ligand. Flexible protein side chains. Maintained by the Molecular Graphics Laboratory, The Scripps Research Institute, la Jolla.
DOCK. Anchor-and-Grow based docking program. Free for academic usage. Flexible ligand. Flexible protein. Maintained by the Soichet group at the UCSF.
GOLD. GA based docking program. Flexible ligand. Partial flexibility for protein. Product from a collaboration between the university of Sheffield, GlaxoSmithKline plc and CCDC.
SCIGRESS. Desktop/server molecular modeling software suite employing linear scaling semiempirical quantum methods for protein optimization and ligand docking. Developed and distributed by Fujitsu, Ltd.
GlamDock. Docking program based on a Monte-Carlo with minimization (basin hopping) search in a hybrid interaction matching / internal coordinate search space. Part of the Chil2 suite. Open for general research.
FlexAID. A small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function. The pairwise energy parameters were derived from a large dataset of true positive poses and negative decoys from the PDBbind database through an iterative process using Monte Carlo simulations. Precompiled Linux, MacOS and Windows versions are made available by the University of Sherbrooke, Canada.
GEMDOCK. Generic Evolutionary Method for molecular DOCKing. Program for computing a ligand conformation and orientation relative to the active site of target protein
iGEMDOCK. Graphic environment for the docking, virtual screening, and post-screening analysis. Free for non commercial researches. For Windows and Linux.
HomDock. Progam for similarity-based docking, based on a combination of the ligand based GMA molecular alignment tool and the docking tool GlamDock. Part of the Chil2 suite. Open for general research.
ICM. Docking program based on pseudo-Brownian sampling and local minimization. Ligand and protein flexible. Provided by MolSoft.
FlexX, Flex-Ensemble (FlexE). Incremental build based docking program. Flexible ligand. Protein flexibility through ensemble of protein structure. Provided by BioSolveIT.
Fleksy. Program for flexible and induced fit docking using receptor ensemble (constructed using backbone-dependent rotamer library) to describe protein flexibility. Provided by the Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen.
FITTED. (Flexibility Induced Through Targeted Evolutionary Description). Suite of programs to dock flexible ligands into flexible proteins. This software relies on a genetic algorithm to account for flexibility of the two molecules and location of water molecules, and on a novel application of a switching function to retain or displace water molecules and to form potential covalent bonds (covalent docking) with the protein side-chains. Part of the Molecular FORECASTER package and FITTED Suite. Free for an academic site license (excluding cluster).
VLifeDock. Multiple approaches for protein - ligand docking. Provides three docking approches: Grid based docking, GA docking and VLife's own GRIP docking program. Several scoring functions can be used: PLP score, XCscore and Steric + Electrostatic score. Available for Linux and Windows. Provided by VLife.
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.
DAIM-SEED-FFLD. Free open source fragment-based docking suite. The docking is realized in three steps. DAIM (Decomposition And Identification of Molecules) decomposes the molecules into molecular fragments that are docked using SEED (Program for docking libraries of fragments with solvation energy evaluation). Finally, the molecules are reconstructed ''in situ'' from the docked fragments using the FFLD program (Program for fragment-based flexible ligand docking). Deve