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.
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.
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 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.
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.
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.
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.
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.
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.