An information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. HADDOCK can deal with a large class of modeling problems including protein-protein, protein-nucleic acids and protein-ligand complexes.
Predicts protein–protein interactions (PPIs). Cluspro is an automated web server for protein-protein docking. The software can discriminate putative structures generated by the user, executing any one of the server-compatible docking algorithms. Additional functions allows users to perform a structure modification, specify attraction and repulsion or define pairwise distance restraints.
Allows structural prediction of protein-protein interactions (PPIs). pyDock is a docking protocol scoring docking poses generated with FFT-based algorithms. The software contains the pyDockNIP module for predicting interface residues in a given protein-protein complex. It can improve the characterization of genomic variants involved in PPIs, especially in cases with low or limited structural information on the binding complexes. The pyDockWEB server allows the academic community to use the pyDock rigid-body docking and scoring method.
Predicts structures of transmembrane protein complexes. DOCK/PIERR is a docking algorithm that predicts, in atomic resolution, the structure of the complex formed by two proteins, given their individual tertiary structure. The conformational space of complexes is sampled exhaustively using Fast Fourier Transforms. The software uses the potentials Protein Interaction Energy (PIE) and Protein Interfaces, Surfaces and Assemblies (PISA) for scoring residue and atomic contacts at protein interfaces.
Generates accurate structures of protein-protein complexes. PIPER is a Fast Fourier Transform (FFT)-based protein docking program, extended to be used with pairwise interaction potentials and based on docking code from the Vajda lab at Boston University. The software allows to improve results docking an antigen to an antibody or docking to form a dimer or trimer.
A server for protein docking based on a free rigid-body docking strategy. It relies on the integration of various components for decoy generation and scoring. Particularly, the combination of the SOAP-PP, FRODOCK and InterEvScore makes it very efficient for the identification of complex conformations not undergoing large conformational changes. The server has many advantages: a user-specific workspace for easy job management, fast evaluation of several tens of thousands of models, high success rates of the consensus method and a user-friendly graphical interface. In 91% of all complexes tested in the benchmark, at least one residue out of the 10 predicted is involved in the interface, providing useful guidelines for mutagenesis. InterEvDock is able to identify a correct model among the top10 models for 49% of the rigid-body cases with evolutionary information, making it a unique and efficient tool to explore structural interactomes under an evolutionary perspective.
Allows users to predict complex structures. ATTRACT is a program available through a desktop version and a web application. It can tackle a large variety of docking problems, due to an extensive set of features and options. Its web interface provides a convenient way to set up an ab initio two-body protein-protein docking protocol.
Allows users to perform assembly tasks and to simplify developments without sacrificing speed for correctness. PTools is able to deal with both coarse-grained as well as atomic resolution representations of biomolecular structures. It can be used for docking searches and provides tools to load and manipulate structures. This tool can be useful for preparation, setup, running and analysis of docking minimizations.
Assists in finding a minimum free-energy complex structure. RosettaDock is a multi-start, multi-scale Monte Carlo based algorithm which searches the rigid-body and side-chain conformational space of two interacting proteins. It can be combined with other docking servers, using its capability of local searches to refine proposed docking positions. It also includes a simple interface and computing resources.
Aims to reduce visual “clutter” by using a single-window approach. Sculptor is a multi-scale modeling program which combines various visualization techniques with pattern matching and feature extraction algorithms. The main user interface elements are arranged around a central 3D graphics area, using non-overlapping frames. Using graphics card processors (GPUs) acceleration, this method is able to display molecular systems with hundreds of thousands of atoms in various rendering styles.
A web server to predict the binding affinity of protein-protein complexes from their three-dimensional structure. The PRODIGY server implements our simple but highly effective predictive model based on intermolecular contacts and properties derived from non-interface surface.
A computational multiple protein docking algorithm that builds models of multimeric complexes by effectively reusing pairwise docking predictions of component proteins. A genetic algorithm is applied to explore the conformational space followed by a structure refinement procedure.
Generates ligand orientations using geometric hashing and the 3D Zernike descriptor. LZerD is a protein-protein docking program that represents protein surfaces using 3D Zernike descriptors (3DZD), which are based on a mathematical series expansion of a 3D function. The 3DZD are a soft representation of the surface shape, which confers tolerance to the conformational changes associated with binding. The software generates docking decoys.
Allows determination of cyclically symmetric homomultimers. SymmDock a priori limits its transformational search space only to symmetric transformations. It is based on a geometry docking algorithm. This tool is able to generate a candidate set of transformations by utilizing local feature matching. It products a web page allowing display of predicted solutions. The whole multimer is created for each solution.
Combines a distant-dependent knowledge-based potential with Fast Fourier Transform (FFT)-accelerated exhaustive sampling on spherical grids. Our potential approximates the binding free energy of protein complexes. We deduce its polynomial expansion coefficients using a training set of protein–protein interfaces and a novel convex optimization problem inspired by a robust machine learning technique. Then, we insert the obtained expansion coefficients into the Hex exhaustive sampling library. This is the first attempt to combine data-driven arbitrary-shaped potentials with a FFT-exhaustive search.
Finds docking transformations that yield good molecular shape complementarity. A wide interface is ensured to include several matched local features of the docked molecules. PatchDock divides the Connolly dot surface representation of the molecules into concave, convex and flat patches. Then, complementary patches are matched to generate candidate transformations. Each candidate is further evaluated by a scoring function that considers both geometric fit and atomic desolvation. An root mean square deviation clustering is applied to the candidate solutions to discard redundant solutions. PatchDock performs structure prediction of protein–protein and protein–small molecule complexes.
Provides a rotational protein–protein docking approach. FRODOCK is a web application that explore and select protein–protein models and interactively screen them against experimental distance constraints. This method optimizes van der Waals, desolvation, and electrostatics interaction potentials. It combines the capability to express the interaction terms into 3D grid-based potentials with the of a spherical harmonics-based rotational search.
Calculates bimolecular protein–protein association rate constants. SDA has been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration-dependent effects. It offers the possibility to account for different conformations of the solutes and parallelization on multi-core processors for bimolecular simulations.
Allows visualization and prediction of potential interaction regions at protein surfaces. ArDock is a web application that allows the manipulation of different proteins and set of protein chains. It includes features for detecting interface residues using a structural information. This tool does not perform explicit clustering of surface residues to predict interaction patches.
Refines, scores and ranks a subset of docking poses generated during sampling search. PROBE is a web service performs ranking of pruned poses, after structure refinement and scoring using a regression model for geometric compatibility, and normalized interaction energy. The former uses an interface area based edge-scoring function to eliminate >95% of the poses generated during docking search. The method has been shown to efficiently score docking poses using its simple scoring function.
Selects a subset of docking poses generated during sampling search. PRUNE uses a single parameter, interface-area-based edge function that has been shown to time-efficiently select subsets of docking poses for improved scoring and ranking of poses. It calculates the intelligence artificial (IA) of the unrefined docking poses generated between the reference (static) and the mobile molecule. The tool was tested on 922 bound, and 77 unbound binary docking targets covering 193–7658A2 interface ranges.
Provides a user-friendly web access to a hybrid algorithm of template-based modeling and free docking for protein-protein and protein-DNA/RNA complexes. HDOCK is a docking server that efficiently integrates various components including sequence search, template selection and model building. The predictive power of the HDOCK server can be also improved by ranking first of the template-based model.
Corrects protein-protein complex orientations. FunHunt is also able to choose the near-native orientation among models created by algorithms other than RosettaDock, demonstrating its general applicability for model selection. It then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one).
Identifies hinge regions and rigid parts using HingeProt, an algorithm for protein hinge prediction using elastic network models. FlexDock is a ﬂexible docking algorithm that handles docking with hinge-bending motions in one of the molecules without increasing the order of computational complexity. It docks the input molecules while explicitly considering the hinges and possible protein motions.
A tool to rank protein-protein docked models based on predicted partner-specific protein interface residues. DockRank uses PS-HomPPI to predict the partner-specific protein interface residues for the docked model. By comparing the predicted interfaces and the interfaces in the docked models, DockRank gives a rank for the docked models. The models with high interface similarity with the predicted interfaces are ranked top.
Allows users to predict the structures of cyclically symmetric multimers. M-ZDOCK is protein docking program, based on a Fast Fourier Transform (FFT), that consists of a derivation of the ZDOCK algorithm. The application aims to perform a simplified search for the correct complex by using Cn symmetry properties. It can be used for protein modeling, protein pathways studies and protein or peptide ligand docking.
Offers an application for fitting X-ray crystal structures into low-resolution density maps. ADP_EM is a method that constitutes a general 3D registration algorithm. It was developed on a combination of fast rotational matching (FRM) method with translational scans. This methodology is an all-purpose registration tool that can be readily applied to any 3D rigid-body registration problem. It could also be extended to other fields.
A web application to easily and effectively analyse and visualize the interface in biological complexes (such as protein-protein, protein-DNA and protein-RNA complexes), by making use of intermolecular contact maps. The user only needs to download input files directly from the wwPDB or upload her/his own PDB formatted files and to specify the chain identifiers for the molecules involved in the interaction to be analysed. Please note that more chains can be selected for each interacting partner.
Provides each residue with the opportunity to contribute in its most favorable local structural environment. InterEvScore is a scoring function using a coarse-grained statistical potential including two- and three-body interactions. It achieves significant improvement over traditional scoring functions on the 54 test cases from the docking benchmark with available coupled multiple sequence alignments (MSAs) and near-native decoys.
An algorithm for modeling of multimolecular protein complexes. DockStar integrates both high resolution data of the individual subunits and low resolution data, such as the complex interaction graph and chemical cross-links.
A graphical interface for the PyRosetta framework that presents easy-to-use controls for several of the most widely-used Rosetta protocols alongside a sophisticated selection system utilizing PyMOL as a visualizer. InteractiveROSETTA is also capable of interacting with remote Rosetta servers, facilitating sophisticated protocols that are not accessible in PyRosetta or which require greater computational resources.
A scoring function that predicts the absolute quality of docking model measured by a novel protein docking quality score (DockQ). ProQDock uses support vector machines trained to predict the quality of protein docking models using features that can be calculated from the docking model itself. By combining different types of features describing both the protein–protein interface and the overall physical chemistry, it was possible to improve the correlation with DockQ from 0.25 for the best individual feature (electrostatic complementarity) to 0.49 for the final version of ProQDock. ProQDock performed better than the state-of-the-art methods ZRANK and ZRANK2 in terms of correlations, ranking and finding correct models on an independent test set. Finally, we also demonstrate that it is possible to combine ProQDock with ZRANK and ZRANK2 to improve performance even further.
Provides a dimensionality reduction of conformational space in flexible protein docking. cNMA determines weights or coefficients for individual modes, and increases protein docking results. It can serve for analyzing protein flexibility in the environment of encounter complexes, and for generating conformational vectors.
Uses an approach for the efficient docking of peptide motifs to their free receptor structures. Using a motif based search, ClusPro PeptiDock can retrieve structural fragments from the Protein Data Bank (PDB) and extract the regions that match the motif. This online method use a Fast Fourier Transform (FFT) based docking method to quickly perform global rigid body docking of these fragments to the receptor.
A web tool for analyzing, comparing and ranking protein-protein and protein-nucleic acid docking models, based on the conservation of inter-residue contacts and its visualization in 2D and 3D interactive contact maps. The user only needs to upload her/his own PDB formatted files and to specify the chain identifiers for the molecules involved in the interaction to be analysed. Please note that more chains can be selected for each interacting partner.
Discriminates the interfaces of biologic homodimers and packing interfaces of a similar size formed by monomeric proteins in crystals. DiMoVo is a web server that compares very favorably with existing methods, especially for difficult cases. Achieves a high accuracy even on crystal dimers that have large interfaces. This application is a method based on the Voronoi tessellation and a coarse-grained modelling of the protein structure.
Allows protein–protein docking. Cell-Dock is a fast Fourier Transform (FFT)-based docking algorithm that generates docking candidates performing a global scan of the translational and rotational space of two molecules based on surface complementarity and electrostatics. The software can run on the PlayStation 3, opening the door to large-scale experiments that may benefit from volunteer-based distributed computing.
Establishes a link between topographic images from atomic force microscopy (AFM) and molecular dynamics of single proteins. DockAFM is an online computational tool that computes the fit of input conformations of a molecule with the topographic surface of AFM images. It can be used to benchmark protein 3D structures or models against an experimental data obtained by AFM. DockAFM uses a real-space description of atoms and surfaces and has been developed as the first step to assemble large macromolecules using their individual constituent.
Allows protein-protein docking. LightDock is based on the Glowworm Swarm Optimization (GSO) algorithm for sampling the translational and rotational space of protein-protein docking, and anisotropic network model (ANM) representation for the inclusion of flexibility. The software allows testing and development of new scoring strategies for protein-protein docking. It can accommodate many different scoring functions (alone or in combination) at different resolution level, and conformational flexibility.