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Protein-Protein Docking Servers:
- ClusPro: (http://nrc.bu.edu/cluster) represents the first fully automated, web-based program for the computational docking of protein structures. Users may upload the coordinate files of two protein structures through ClusPro's web interface, or enter the PDB codes of the respective structures, which ClusPro will then download from the PDB server (http://www.rcsb.org/pdb/). The docking algorithms evaluate billions of putative complexes, retaining a preset number with favorable surface complementarities. A filtering method is then applied to this set of structures, selecting those with good electrostatic and desolvation free energies for further clustering. The program output is a short list of putative complexes ranked according to their clustering properties, which is automatically sent back to the user via email.
- RosettaDock: The RosettaDock protein-protein docking server predicts the structure of protein complexes given the structures of the individual components and an approximate binding orientation. The server uses the Rosetta 2.1 protein structure modeling suite. The RosettaDock server (http://rosettadock.graylab.jhu.edu) identifies low-energy conformations of a protein–protein interaction near a given starting configuration by optimizing rigid-body orientation and side-chain conformations. The server requires two protein structures as inputs and a starting location for the search. RosettaDock generates 1000 independent structures, and the server returns pictures, coordinate files and detailed scoring information for the 10 top-scoring models. A plot of the total energy of each of the 1000 models created shows the presence or absence of an energetic binding funnel. RosettaDock has been validated on the docking benchmark set and through the Critical Assessment of PRedicted Interactions blind prediction challenge.
- ZDOCK, RDOCK: ZDOCK uses a fast Fourier transform to search all possible binding modes for the proteins, evaluating based on shape complementarity, desolvation energy, and electrostatics. The top 2000 predictions from ZDOCK are then given to RDOCK where they are minimized by CHARMM to improve the energies and eliminate clashes, and then the electrostatic and desolvation energies are recomputed by RDOCK (in a more detailed fashion than the calculations performed by ZDOCK). We then tested these programs with a benchmark of 49 non-redundant unbound test cases, where we identified a near-native structure (within 2.5 angstrom from the experimental structure) as the top prediction for 37% of the test cases, and within the top 4 predictions for 49% of the test cases. The superior performance of ZDOCK and RDOCK has also been demonstrated in a community-wide protein docking blind test, CAPRI. Check this out for more details. All software, as well as thebenchmark is freely available to academic users. For basic information on running ZDOCK, see this site.
- GPU.proton.DOCK: (Genuine Protein Ultrafast proton equilibria consistent DOCKing) is a state of the art service for in silico prediction of protein–protein interactions via rigorous and ultrafast docking code. It is unique in providing stringent account of electrostatic interactions self-consistency and proton equilibria mutual effects of docking partners. GPU.proton.DOCK is the first server offering such a crucial supplement to protein docking algorithms—a step toward more reliable and high accuracy docking results. The code (especially the Fast Fourier Transform bottleneck and electrostatic fields computation) is parallelized to run on a GPU supercomputer. The high performance will be of use for large-scale structural bioinformatics and systems biology projects, thus bridging physics of the interactions with analysis of molecular networks. We propose workflows for exploring in silico charge mutagenesis effects. Special emphasis is given to the interface-intuitive and user-friendly. The input is comprised of the atomic coordinate files in PDB format. The advanced user is provided with a special input section for addition of non-polypeptide charges, extra ionogenic groups with intrinsic pKa values or fixed ions. The output is comprised of docked complexes in PDB format as well as interactive visualization in a molecular viewer. GPU.proton.DOCK server can be accessed athttp://gpudock.orgchm.bas.bg/.
- GRAMM-X: Protein docking software GRAMM-X and its web interface (http://vakser.bioinformatics.ku.edu/resources/gramm/grammx) extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations. Docking problems submitted to GRAMM-X server are processed by a 320 processor Linux cluster. The server was extensively tested by benchmarking, several months of public use, and participation in the CAPRI server track.
- HexServer: HexServer (http://hexserver.loria.fr/) is the first Fourier transform (FFT)-based protein docking server to be powered by graphics processors. Using two graphics processors simultaneously, a typical 6D docking run takes ∼15 s, which is up to two orders of magnitude faster than conventional FFT-based docking approaches using comparable resolution and scoring functions. The server requires two protein structures in PDB format to be uploaded, and it produces a ranked list of up to 1000 docking predictions. Knowledge of one or both protein binding sites may be used to focus and shorten the calculation when such information is available. The first 20 predictions may be accessed individually, and a single file of all predicted orientations may be downloaded as a compressed multi-model PDB file. The server is publicly available and does not require any registration or identification by the user.
- 3D-Garden: a system for modelling protein–protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm. 3DGarden is an integrated software suite for performing protein-protein and protein-polynucleotide docking. For any pair of biomolecules structures specified by the user, 3DGarden's primary function is to generate an ensemble of putative complexed structures and rank them. The highest-ranking candidates constitute predictions for the structure of the complex. 3DGarden cannot be used to decide whether or not a particular pair of biomolecules interacts. Complexes of protein and nucleic acid chains can also be specified as individual interactors for docking purposes.
List of online docking (protein–ligand) Servers:
- ParDock
Its an Automated Server for Protein Ligand Docking. Its an an all-atom energy based Monte Carlo, rigid docking, which predicts the ligand binding mode in receptor target site
Supporting Reference:
Gupta, A. Gandhimathi, A. Sharma, P. and Jayaram, B. (2007) ParDOCK: An All Atom Energy Based Monte Carlo Docking Protocol for Protein-Ligand Complexes. Protein and Peptide Letters, 2007, 14, 7, 632-646.
- Dock Blaster
DOCK Blaster is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). DOCK Blaster will dock and score each molecule against your target and provide you with a ranked list which you may review and prioritize for purchase and testing. Dock Blaster also provide ZINC database.
Supporting Reference: Irwin, Shoichet, Mysinger et al., “Automated docking screens: a feasibility study.”, J. Med. Chem. 2009, 52(18), pp 5712-5720.
- Swiss Dock
SwissDock is based on the docking software EADock DSS, whose algorithm consists of the following steps: many binding modes are generated either in a box (local docking) or in the vicinity of the target cavities (blind docking). simultaneously, their CHARMM energies are estimated on a grid. the binding modes with the most favorable energies are evaluated with FACTS, and clustered. the most favorable clusters are dumped in a file.
SwissDock
Supporting Reference: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W270-7. Epub 2011 May 29. SwissDock, a protein-small molecule docking web service based on EADock DSS. Grosdidier A, Zoete V, Michielin O.
- MEDOCK:
The MEDock (Maximum-Entropy based Docking) web server is aimed at providing an efficient utility for prediction of ligand binding site. A major distinction in the design of MEDock is that its global search mechanism is based on a novel optimization algorithm that exploits the maximum entropy property of the Gaussian distribution.
Supporting Reference:
Darby Tien-Hau Chang, Yen-Jen Oyang, and Jung-Hsin Lin, MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm. Nucleic Acids Res. 2005 July 1; 33(Web Server issue): W233–W238.
- DOCKING Server
DockingServer offers a web-based, easy to use interface that handles all aspects of molecular docking from ligand and protein set-up. While its user friendly interface enables docking calculation and results evaluation carried out by researchers coming from all fields of biochemistry, DockingServer also provides full control on the setting of specific parameters of ligand and protein set up and docking calculations for more advanced users.
Supporting Reference:
Bikadi, Z., Hazai, E. Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock J. Cheminf. 1, 15 (2009)
- patchDock:
PatchDock algorithm is inspired by object recognition and image segmentation techniques used in Computer Vision. Docking can be compared to assembling a jigsaw puzzle. When solving the puzzle we try to match two pieces by picking one piece and searching for the complementary one. We concentrate on the patterns that are unique for the puzzle element and look for the matching patterns in the rest of the pieces. PatchDock employs a similar technique. Given two molecules, their surfaces are divided into patches according to the surface shape. These patches correspond to patterns that visually distinguish between puzzle pieces. Once the patches are identified, they can be superimposed using shape matching algorithms. The algorithm has three major stages:
Supporting Reference:
Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucl. Acids. Res. 33: W363-367, 2005.[ Full text ]
- FireDock
The FireDock server addresses the refinement problem of protein-protein docking solutions. The method simultaneously targets the problem of flexibility and scoring of solutions produced by fast rigid-body docking algorithms. Given a set of up to 1000 potential docking candidates, FireDock refines and scores them according to an energy function, spending about 3.5 seconds per candidate solution. To the best of our knowledge, this is the first webserver that allows performing large-scale flexible refinement and scoring of docking solutions online.
Supporting Reference:
N. Andrusier, R. Nussinov and H. J. Wolfson. FireDock: Fast Interaction Refinement in Molecular Docking. Proteins 2007, 69(1):139-59.