Can anyone tell me the best docking tool is? Please suggest me the best tool or software with the links, if you have.
Thanks in advance.
There are several paid and freely available software for docking and scoring for ligand and receptor. Some of the prominent one where you can also do flexible docking are FlexX, Discovery Studio, Glide etc which show good correlation with the experimental results. However they are paid. there are some free software with good correlation as well one is Autodock but to learn that it will take time. You can also use pardock freely available at http://www.scfbio-iitd.res.in/dock/pardock.jsp . which also shows good correlation developed by our group. Just look for the format of input file it use of this software is relatively easy. Best!
For me, AutoDock is still a standard for local docking. For blind docking, the SwissDock (http://www.swissdock.ch) server is an excellent tool. It is anyhow very recommended to start with multiple docking engines/functions before selecting one and eventually put some constraints. No need to go for commercial products. You got plenty of free alternatives for academic research. Please have a look at http://click2drug.org for a complete list (with links) of docking softwares and not only.
Enjoy!
AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use
http://vina.scripps.edu/
there are several other tools for docking available like GOLD and discovery studio, but they are paid. Besides as Mr. Arvind said, i feel that Vina is the most frequently used tool for docking.
I suggest you use Audotock Vina. I have used several docking softwares, but vina has outperformed the others. My personal experience, at least.
use Molegro virtual docker..they will provide you one month trial...it is easy to use and best way to analysis the docking pose.....http://www.molegro.com/trial.php
There are several other tools for docking are available but Autodock is best.
Docking is an inexact science. We use a combination of Autodock (free) and Schrodinger's Glide. It is good to use two different methods and see if they agree.
You may go for following for freely available:
Autodock, Zdock (windows/linux)
Hex
website: www.dockingserver.com
Commercial available:
Schrodinger : glide
Discovery Studio
Molegro
Autodock, Haddock and RosettaDock are very good.
3D-Dock is also good, especially if you have experimental constraints.
Hex-dock.
One of the best is Molsoft ICM. Glide, Molegro and Autodock perform very well too.
I suggest u to go for molegro Virtual Docking software (Renee thompson) which is easy and user friendly for docking various ligands and protein I have used this software for my inhibitory compounds and get data well u can get a free licensed evaluated copy with fully activated features and u can even publish your data in journals (Some softwares wont allow to publish there results in journal)
15 minutes ago
Yes, Molegro VD as Filip and Anvesh mentioned above is a very capable software. In addition, to my best knowledge this is the only available at the moment CUDA ported docking software. A regular docking by Molegro VD takes 2 min against 7s using the Cuda version.
I personally recommend HADDOCK, it has a large user base, mailing lists for help, continuous development and is coded such that you can add your own custom code to it quite easily (if you know Python). It has the benefit of EU funding so you can use other people's clusters for fast processing and has always scored well on the CAPRI tests; which after all, you want accurate models at the end.
Schrodinger glide is best, If you want to use freeware you can use AutoDock. It is best in freeware. Easy and user friendly.
I agree autodock vina is good not only terms of speed but also accuracy over autodock. Additionally it is freely available
It depends on your needs. If you have a protein with a known binding site and you are looking for a software to predict the correct binding mode of your ligand, the best choice is GOLD. Unfortunately GOLD is expensive and present some limitations if you are looking for a software to tell you teh affinity of your ligand to the target. VINA and AutoDock are better in this case (and they are free).
it depends on your need.if you are looking for fast and accurate docking go for Autodock vina and if you are looking for fine docking go for autodock4 ..you can use both the tool at once in a pipeline
The type of docking tool selection depends upon the type of docking you are looking for. For protein-ligand docking, you can use DOCK or Autodock softwares. For protein-protein docking, you might use clusterpro or firedock tools. Regarding interpretations of docking complexes, Schrodinger package or Gold softwares might be tried. Even Zdock or Swissdock online tools might also be used for protein-ligand docking.
Yes it is true many softwares are available. It is depend very much up on once need / purpose sp i recommend one can work with thoes availebale in public domain for free usage like autodock
I often come accross such questions as to what is the best server and all...I think the easiest and most reliable way of looking at it is to take a look at the latest CASP predictions. However, to answer you more to the point:
If you are doing constraint free blind docking then you have got to use more than one server(my choices would be Cluspro, Z dock, Autodock and Hex) and look at atleast the top ten output files from each of these and alongwith any possible biochemical interaction data available for your protein of interest define the likely interaction interface and the residues around it. Then use this information to perform a constraint based docking on Haddock. This is how "I" would go about it.
If you are already aware of the constraints you can directly use Haddock or Cluspro in advanced modes. However, it might make sense to simulate your docking output once it is obtained or refine it in docking refinement program.
For BlindDocking go for SwissDock or PatchDock, but these are online servers.
For Docking at targeted site on protein, go for AutoDockTools, (AutoDock Vina is an alternate)..
Has anyone use Rosetta 3.1? would you recommend using autodock and rosetta 3.1?
AutoDock, AutoDock Vina, FlexX, SurflexX, Gold, Scigress-Dock, Dock. Use multiple tool, select those which able to mimic actual conformation, use known complex crystallographic data having bound known drug or active compound. Lowest RMSD should be there. Use positive control for validating any docking software. Mostly all docking tools show the binding affinity and able to mimic ~40-50% actual binding mode. No single tool work in all protein targets, use wisely. No option of negative control check. In docking simulation even negative control drug/compound show good binding affinity with good docking score, although its a false positive result. Be alert...ask for negative data set docking exercise evaluation, no software company talk about on this..
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==== Docking - Software ====
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). Developed and maintained by the Computational Structural Biology of ETH, Zurich, Switzerland.
Autodock Vina. MC based docking software. Free for academic usage. Flexible ligand. Flexible protein side chains. Maintained by the Molecular Graphics Laboratory, The Scripps Research Institute, la Jolla.
VinaMPI. Massively parallel Message Passing Interface (MPI) program based on the multithreaded virtual docking program AutodockVina. Free and open source. Provided by the University of Tennessee.
FlipDock. GA based docking program using FlexTree data structures to represent a protein-ligand complex. Free for academic usage. Flexible ligand. Flexible protein. Developed by the Department of Molecular Biology at the Scripps Research Institute, la Jolla.
PharmDock. A protein pharmacophore-based docking program. PharmDock and a PyMOL plugin are made freely available by the Purdue University, West Lafayette, USA.
FRED. FRED performs a systematic, exhaustive, nonstochastic examination of all possible poses within the protein active site, filters for shape complementarity and pharmacophoric features before selecting and optimizing poses using the Chemgauss4 scoring function. Provided by OpenEye scientific software.
POSIT. POSIT uses the information from bound ligands to improve pose prediction. Using a combination of approaches, including structure generation, shape alignment and flexible fitting, a ligand of interest is compared to bound ligands and its similarity to such both guides the nature of the applied algorithm and produces an estimate. Both 2D and 3D similarity measures are used in this reliability index. Provided by OpenEye scientific software.
HYBRID. Docking program similar to FRED, except that it uses the Chemical Gaussian Overlay (CGO) ligand-based scoring function. Provided by OpenEye scientific software.
idock. Free and open source multithreaded virtual screening tool for flexible ligand docking for computational drug discovery. Developed by the Chinese university of Hong Kong.
POSIT. Ligand guided pose prediction. POSIT uses bound ligand information to improve pose prediction. Using a combination of several approaches, including structure generation, shape alignment and flexible fitting, it produces a predicted pose whose accuracy depends on similarity measures to known ligand poses. As such, it produces a reliability estimate for each predicted pose. In addition, if provided with a selection of receptors from a crystallographic series, POSIT will automatically determine which receptor is best suited for pose prediction. Provided by OpenEye scientific software.
Rosetta Ligand. Monte Carlo minimization procedure in which the rigid body position and orientation of the small molecule and the protein side-chain conformations are optimized simultaneously. Free for academic and non-profit users.
Surflex-Dock. Docking program based on an idealized active site ligand (a protomol), used as a target to generate putative poses of molecules or molecular fragments, which are scored using the Hammerhead scoring function. Distributed by Tripos.
CDocker. CHARMm based docking program. Random ligand conformations are generated by molecular dynamics and the positions of the ligands are optimized in the binding site using rigid body rotations followed by simulated annealing. Provided by Accelrys.
LigandFit. CHARMm based docking program. Ligand conformations generated using Monte-Carlo techniques are initially docked into an active site based on shape, followed by further CHARMm minimization. Provided by Accelrys.
rDock. Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids. Free and open source.Developed by the University of Barcelona.
MOE. Suite of medicinal chemistry tools like Ligand-Receptor Docking, Protein/Ligand Interaction Diagrams, Contact Statistics, Electrostatic, & Interaction Maps, LigX (Ligand Optimization in Pocket), Ligand & Structure-Based Scaffold Replacement, Multiple Molecule Flexible Alignment, Conformation Generation, Analysis, & Clustering, Active Site Detection & Visualization, Multi-Fragment Search, Ligand & Structure-Based Query Editor, High-Throughput Conformation Generation, Pharmacophore Search. Distributed by Chemical Computing Group.
Lead Finder. program for molecular docking, virtual screening and quantitative evaluation of ligand binding and biological activity.Distributed by Moltech. For Windows and linux.
YASARA Structure. Adds support for small molecule docking to YASARA View/Model/Dynamics using Autodock and Fleksy. Provided by YASARA.
ParaDockS. ParaDockS includes algorithms for protein-ligand docking and is organized that every newly developed scoring function can be immediately implemented. Furthermore, interaction-based classifier, trained on a target-specific knowledge base can be used in a post-docking filter step. An implementation and validation of target-biased scoring methods within the open-source docking framework is implemented. developed and provided free of charge by the University of Halle-Wittenberg, Germany.
GalaxyDock. Protein-ligand docking program that allows flexibility of pre-selected side-chains of ligand. Developed by the Computational Biology Lab, Department of Chemistry, Seoul National University.
MS-Dock. Free multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening.
FINDSITE-LHM. Homology modeling approach to flexible ligand docking. It uses a collection of common molecule substructures derived from evolutionarily related templates as the reference compounds in similarity-based ligand binding pose prediction. It also provides a simple scoring function to rank the docked compounds. Freely available to all academic users and not-for-profit institutions. Provided by the Skolnick Research Group.
BetaDock. Molecular docking simulation software based on the theory of Beta-complex.
ADAM. Automated docking tool. Can be used for vHTS. Distributed by IMMD.
hint!. (Hydropathic INTeractions). Estimates LogP for modeled molecules or data files, numerically and graphically evaluates binding of drugs or inhibitors into protein structures and scores DOCK orientations, constructs hydropathic (LOCK and KEY) complementarity maps that can be used to predict a substrate from a known receptor or protein structure or to propose the hydropathic structure from known agonists or antagonists, and evaluates/predicts effects of site-directed mutagenesis on protein structure and stability.
DockVision. Docking package including Monte Carlo, Genetic Algorithm, and database screening docking algorithms.
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.
ADDock. Anchor dependent molecular docking method. Distributed by Biodelight.
EADock. Hybrid evolutionary docking algorithm with two fitness functions, in combination with a sophisticated management of the diversity. EADock is interfaced with the CHARMM package for energy calculations and coordinate handling.
EUDOC. Program for identification of drug interaction sites in macromolecules and drug leads from chemical databases.
FLOG. Rigid body docking program using databases of pregenerated conformations. Developed by the Merck Research Laboratories.
Hammerhead. Automatic, fast fragment-based docking procedure for flexible ligands, with an empirically tuned scoring function and an automatic method for identifying and characterizing the binding site on a protein.
ISE-Dock. Docking program which is based on the iterative stochastic elimination (ISE) algorithm.
ASEDock. Docking program based on a shape similarity assessment between a concave portion (i.e., concavity) on a protein and the ligand. Developed by yoka Systems.
HADDOCK. HADDOCK (High Ambiguity Driven biomolecular DOCKing) is an approach that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions. First developed from protein-protein docking, it can also be applied to protein-ligand docking. Developed and maintained by the Bijvoet Center for Biomolecular Research, Netherlands.
Computer-Aided Drug-Design Platform using PyMOL. PyMOL plugins providing a graphical user interface incorporating individual academic packages designed for protein preparation (AMBER package and Reduce), molecular mechanics applications (AMBER package), and docking and scoring (AutoDock Vina and SLIDE).
Autodock Vina plugin for PyMOL. Allows defining binding sites and export to Autodock and VINA input files, doing receptor and ligand preparation automatically, starting docking runs with Autodock or VINA from within the plugin, viewing grid maps generated by autogrid in PyMOL, handling multiple ligands and set up virtual screenings, and set up docking runs with flexible sidechains.
GriDock. Virtual screening front-end for AutoDock 4. GriDock was designed to perform the molecular dockings of a large number of ligands stored in a single database (SDF or Zip format) in the lowest possible time. It take the full advantage of all local and remote CPUs through the MPICH2 technology, balancing the computational load between processors/grid nodes. Provided by the Drug Design Laboratory of the University of Milano.
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.
BDT. Graphic front-end application which control the conditions of AutoGrid and AutoDock runs. Maintained by the Universitat Rovira i Virgili,
Web services
SwissDock. SwissDock, a web service to predict the molecular interactions that may occur between a target protein and a small molecule.
DockingServer. DockingServer offers a web-based, easy to use interface that handles all aspects of molecular docking from ligand and protein set-up.
1-Click Docking. Free online molecular docking solution. Solutions can be visualized online in 3D using the WebGL/Javascript based molecule viewer of GLmol. Provided by Mcule.
Blaster. Public access service for structure-based ligand discovery. Uses DOCK as the docking program and various ZINC Database subsets as the database.Provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF).
Pardock. All-atom energy based Monte Carlo, rigid protein ligand docking, implemented in a fully automated, parallel processing mode which predicts the binding mode of the ligand in receptor target site. Maintained by the Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi.
FlexPepDock. High-resolution peptide docking (refinement) protocol, implemented within the Rosetta framework. The input for this server is a PDB file of a complex between a protein receptor and an estimated conformation for a peptide.
PatchDock. Web server for structure prediction of protein-protein and protein-small molecule complexes based on shape complementarity principles.
MEDock. Maximum-Entropy based docking web server for efficient prediction of ligand binding sites.
BSP-SLIM. Web service for blind molecular docking method on low-resolution protein structures. The method first identifies putative ligand binding sites by structurally matching the target to the template holo-structures. The ligand-protein docking conformation is then constructed by local shape and chemical feature complementarities between ligand and the negative image of binding pockets. Provided by the University of Michigan.
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.
GPCRautomodel. Web service that automates the homology modeling of mammalian olfactory receptors (ORs) based on the six three-dimensional (3D) structures of G protein-coupled receptors (GPCRs) available so far and (ii) performs the docking of odorants on these models, using the concept of colony energy to score the complexes. Provided by INRA.
iScreen. Web service for docking and screening the small molecular database on traditional Chinese medicine (TCM) on user's protein. iScreen is also implemented with the de novo evolution function for the selected TCM compounds using the LEA3D genetic algorithm
idTarget. Web server for identifying biomolecular targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach. Maintained by the National Taiwan University.
MetaDock. Online docking solution and docking results analysis service. Docking is done with GNU/GPL-licensed AutoDock v.4 and Dock6 under academic license
Score. Allows to calculate some different docking scores of ligand-receptor complex that can be submitted as a whole file containing both interaction partners or as two separated files. The calculation phase is provided by VEGA. Provided by the Drug Design Laboratory of the University of Milano.
Pose & Rank. Web server for scoring protein-ligand complexes. Provided by the laboratory of Andrej Sali.
PLATINUM. Calculates hydrophobic properties of molecules and their match or mismatch in receptor–ligand complexes. These properties may help to analyze results of molecular docking.
All the best!
Dear Mohsin Yousuf Lone,
Please develop the good habit to cite your sources. Your list is a copy/paste of click2drug.
Please have a look at http://click2drug.org for an updated list (with links) of docking softwares and not only.
Enjoy!
Antoine.
There are lots of tools available some are free and some commercial. You can prefer as per your budget. Both category give good result. PyRx and Discovery Studio are awesome tool for docking. I like to use multiple docking tool to validate my result.
As per my suggestion there are several docking softwere are available but now a day's mostly used as a Autodock vina and PyRX and GOLD.That can be most accurate result of your Docking. result can be analyzed by Pymol and Discovery studio .
According to recent articles GOLD, Glide, Molsoft ICM and Surflex as well as LeDock are among the favorite docking tools which can estimate the binding site and (conventional) free energies with high accuracy. Autodock is no longer thought to be an accurate docking software but still lots of articles are published with this program because of its free license.
Please take a look at these articles for further information:
Article Software for Molecular Docking: A review
Article A detailed comparison of current docking and scoring methods...
Article Comparing protein-ligand docking programs is difficult
Article Benchmark of four popular virtual screening programs: constr...
Here are some tools name along with the URLS for docking.
1) Pyrx (https://pyrx.sourceforge.io/)
2) Swissdock (http://www.swissdock.ch/)
3) Autodock
i think its good time to start writing software Comparison, some thing like this:
https://en.wikipedia.org/wiki/Comparison_of_statistical_packages
there are List of protein-ligand docking software
https://en.wikipedia.org/wiki/List_of_protein-ligand_docking_software
Which docking software is downloadable free of cost and is also easy to use. Please suggest.
Hello
CASTp, Autodock vina, Swissmodel, Qsite, Chimera, RasMol or JMOL, MOE, BIOVIA Discovery Studio.
Check in these links. It might help you.
https://www.click2drug.org/
Good Luck.
Hello,
I'm have a real problem in the instalations of auto dock. Every time i try, only open a MSdos Window and immediately close.
Could someone help me with the installation process? is there any prerequisite to perform before installation
Felipe Oliveira Nunes try reinstalling the program, if the same thing happens again try with other computer or try to install another version of AutoDock tools
use Autodock vina or HEX for getting docking pose and chimera or Discovery Studio for visualization.
you can also go for online docking programs.
There is nothing like best. However you can compare different software for the same target and decide the most suitable. The most ideal tool for docking is the one that can reproduce bioactive conformation of bound ligand with minimum RMSD. GOLD by CCDC and FRED by OpenEye are relatively good. Following link about FRED would provide helpful insight to your question sir. Apart from these Glide tool in Schrodinger Software bundle also have variety of docking option!! They provide evaluation copy upon request through proper channel.
1. Article Docking Challenge: Protein Sampling and Molecular Docking Performance
2. Article FRED Pose Prediction and Virtual Screening Accuracy
3. Article Software for Molecular Docking: A review
Dear All,
Performing docking analyses is hinging on your research goal. Some tools provided flexible docking procedure for the users while others are functioning through rigid ligand/protein docking approach. Short recently, inverse docking method has also been developed for this purpose.
The users are now able to dock various chemical targets against a library of receptors. However, having successful results for docking analyses will require combining other high-throughput methods such as MD simulation and quantum analysis with docking outcomes in order to boost the quality of docking outcomes. Classically, Pyrx ( https://pyrx.sourceforge.io) is one of the most popular tools for doing docking projects. This tool is particularly developed for handling protein-ligand docking projects. Its new version also comprised a protocol and module for inverse docking approach.
For protein-protein docking, I think, however, Cluspro ( https://cluspro.bu.edu/login.php ) is one of the most valuable tools you can count on for evaluating the interaction profile of your receptors and ligands (proteins or peptides).
Another critical note that the respected users should take into consideration with their docking projects is about the way of docking. For some cases you had to apply blind docking protocol whereas for the rest fixed or defined docking protocol should be applied. This issue may have an impact on your final data. So, before any docking process, try to consider this case with your input docking data.
Felipe Oliveira Nunes you have to install first MGtools then you install the Autodocksuit. but you must insert the autodocksuit file in C:\Program Files (x86)\MGLTools-1.5.6
I hope that my answer could help you
The best one as of now is Schrodinger but its quite expensive going for approximately 10, 000 USD.. Autodock will give you what you want and the download is free.... Most appropriate for academia.
■Protein – Ligand
(AutoDock Vina) (offline Software)
( Patchdock) https://bioinfo3d.cs.tau.ac.il/PatchDock/
■Protein – Protein
(ClucPro) https://cluspro.bu.edu/login.php
■Protein – Nucleotide
(HADDOCK) https://haddock.science.uu.nl/
(NPDock) http://genesilico.pl/NPDock
Muhammad Zeeshan Ahmed Hi, may i know why Haddock is not suitable for protein-ligand docking analysis?
This *2012* review article, which was the most recent I could find, shows that DOCK from UCSF is overwhelmingly the most cited docking tool.
Review Article: Article Protein-Ligand Docking in the New Millennium – A Retrospecti...
Hi,
There plenty of tools for docking studies and most of them are mentioned by various experts. I have listed few that may be helpful.
For Protein-Ligand
1. Glide, Maestro, Schrodinger
2. IFD and QPLD are also useful in some cases.
For Protein-Protein-Peptide
1. Prime
2. Haddock
Of course most of the tools listed above are commercial, but has significant results.
Good Luck
I think that Shrodinger software is a best choice, but it is a pity that it is not free.
The list can be classified on several basis; free of cost and paid; easy to use and terminal-based; etc. so the choice is yours.
Hello Rajashri N Bhairamadgi
Docking tools are indeed a great deal pertaining biomolecular studies. Based on the size of the biomolecules i can suggest you 2 efficient docking tools. If the Biomolecules are comparatively bigger, such as in protein-protein or antibody-protein docking HADDOCK 2.4 server can be a great choice. The results from the server come refined and energy-minimized by default. Besides, the active and the passive interacting residues for performing the docking analysis can be known using CPORT, a server from the same developers.
If your Biomolecules are comparatively smaller, as seen in protein-peptide or peptide-peptide docking, i would suggest you to go for Cluspro 2.0. It has been regarded as the most accurate server according to CAPRI evaluations. Even many other researchers have mentioned the same in their previous responses.
Link for HADDOCK 2.4 server:
https://bianca.science.uu.nl/haddock2.4/
Link for CPORT server:
https://alcazar.science.uu.nl/services/CPORT/
Link for Cluspro 2.0 server:
https://cluspro.bu.edu/home.php
Hope it helps.
I have had interesting output from Cluspro 2.0 but I'll always advice that you validate the docking data experimentally if possible by performing site-directed mutagenesis (SDM) for protein-protein, protein-nucleic acid or protein-small molecule interaction followed by assays for instance.
Can anyone recommend a molecular docking program to use for docking protein and long chain polymers (made up of phosphates)?
I do prefer Glide + prime (IFD) or GOLD. However try to dock with many protocols and compare packages to obtain consensus score. Every docking should be validated by MD calculations and should be considered with FEP studies. Then the results are being close to correct. Look here:
Article Advancing Drug Discovery through Enhanced Free Energy Calculations
Article Exponential consensus ranking improves the outcome in dockin...
Article Supervised Consensus Scoring for Docking and Virtual Screening
I have been using both Glide (Schrödinger) and AutoDock Vina (combined with AutoDockTools 4.2).
One can look at it through different perspectives. I think, Glide has a more reliable algorithm whereas AutoDock Vina offers more elementary results.
On the GUI prospect, well there is none for AutoDock Vina since it uses Python so you have to write commands to conduct docking. Schrödinger has a remarkable interface and it is rather easy to use.
Also for screening i would definitely recommend programs such as Schrödinger. With AutoDock Vina it takes a lot of effort to implement similar procedure.
On the other hand, for visualizing Vina results you have to use visualization programs such as Chimera, DS Visualizer etc.
I think AutoDock is very good and it is free also.
autodock.scripps.edu/
You can use Clus Pro, ZDOC, HADDOCK servers for docking, they are free
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