Permits to interactively visualize and analyse molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. UCSF Chimera allows users to incorporate new features. It contains some extensions which permits to visualize large-scale molecular assemblies such as viral coats, and allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions can be used for extend the tool capabilities.
A package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Glide offers the full range of quick and accurate options, from the HTVS to the SP. It also provides virtual screening, accurate binding mode prediction and universal applicability. Comparisons to published data on RMS deviations show that Glide is nearly twice as accurate as GOLD and more than twice compared to FlexX. Glide is also found to be more accurate than the Surflex method.
Allows molecular docking and virtual screening. AutoDock Vina is one of the two generations of distributions of AutoDock. This software uses a sophisticated gradient optimization method in its local optimization procedure. The calculation of the gradient effectively gives the optimization algorithm a “sense of direction” from a single evaluation. By using multithreading, this software can further speed up the execution by taking advantage of multiple CPUs or CPU cores.
Automatically generates 2D ligand-protein interaction diagrams. LigPlot+ is a graphical front-end to the LIGPLOT and DIMPLOT programs. The software allows the 2D representation of multiple ligand protein complexes in a simple and automated manner, without the need of prealigning the protein structure components or using 3D viewers. It enables the direct comparison of multiple, related protein complexes, while allowing for the simultaneous variation of both protein sequence and compound formula.
Provides automated docking tools. AutoDock uses a grid-based method to allow a rapid evaluation of the binding energy of trial conformations. The software can predict bound conformations and binding energies of ligands with macromolecular targets. AutoDockTools, the graphical user interface (GUI) for AutoDock, includes a variety of novel methods for clustering, displaying, and analyzing the results of docking experiments.
Uses procedures for pre-docking minimization and post-docking all-atom in-pocket optimization. Surflex-Dock employs an active site ligand as a target to generate putative poses of molecules or molecular fragments. It utilizes the morphological similarity function and fast pose generation techniques to generate putative alignments of fragments. This tool is based on so-called empirical methods.
Forecasts protein-ligand interactions. MolDock is an application based on an hybrid search algorithm named guided differential evolution combined with a force-field based docking scoring function. This docking platform automates the assignation of charges and protonation states, the prediction of cavities as well as the identification of potential binding sites.