Application Index

Applications for docking a small molecule like drug or ligand onto a large molecule such as an enzyme.

Gold is a genetic algorithm based method for ligand protein docking. It is distributed by the Cambridge Crystallographic Database.
View Application Entry for Gold

LEAPFROG is a powerful, second generation de novo ligand design tool that proposes a series of new, potentially active ligand molecules, even when the receptor structure is not known. LeapFrog generates new compounds by repeatedly making small structural changes, rapidly evaluating the binding energy of the new compound, and keeping or discarding the changes based on the results.
View Application Entry for LEAPFROG

Molegro Virtual Docker is an integrated platform for predicting protein-ligand interactions. Molegro Virtual Docker handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands. Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity.
View Application Entry for Molegro Virtual Docker

SuperStar is a program for generating maps of interaction sites in proteins using experimental information about inter-molecular interactions. The interaction maps that SuperStar generates are therefore fully knowledge-based. SuperStar retrieves its data from IsoStar, CCDC interaction database. IsoStar contains information about non-bonded interactions from both the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB).
View Application Entry for SuperStar

FADE (Fast Atomic Density Evaluator) and PADRE (Pairwise Atomic Density Reverse Engineering) programs are designed to aid in the molecular modeling of proteins. In particular, the programs can rapidly elucidate features of interest such as crevices, grooves and protrusions. The topographical information produced by FADE and PADRE can help researchers easily pinpoint the most prominent features of a protein, regions which are likely to participate in interactions with other molecules. In addition to providing shape descriptors to aid in analyzing single molecules, FADE can directly evaluate the level of shape complementarity for docked protein-protein complexes.
View Application Entry for FADE and PADRE (Fast Atomic Density Evaluator and Pairwise Atomic Density Reverse Engineering)

SHAPE is a package for analysis of molecular surfaces. It includes programs for determining whether a point is in a groove or crevice in a surface, and for determining the largest sphere that can fit at a location. It is free for academic users but a license must be signed and returned before accessing SHAPE.
View Application Entry for SHAPE

DOT is a program for docking macromolecules to other molecules of any size. It runs efficiently on parallel systems ranging from networked workstations to supercomputers.
View Application Entry for DOT (Daughter Of Turnip)

HINT is a software package that utilizes experimental solvent partitioning data as a basis for an empirical molecular interaction model. The program calculates empirical atom-based hydropathic parameters that, in a sense, encode all significant intermolecular and intramolecular non-covalent interactions implicated in drug binding or protein folding. HINT provides tools to estimate numerical binding constants and to visualize hydropathy and hydropathic interactions.
View Application Entry for HINT

Glide is a fast and accurate docking program that addresses a number of problems, ranging from fast database screening to highly accurate docking. The hierarchical filters in Glide ensure a fast and efficient reduction of large data sets to the few drug candidates that bind best with the target.
View Application Entry for Glide

Liaison is a new commercial program for fast estimation of free energy of binding between a receptor and a ligand. Built on the idea of Aqvist et al. [1], the free energy of binding can be approximated by an equation in which only the free and bound states of the ligand are calculated. The method combines high-level molecular mechanics calculations with experimental data to build a scoring function for the evaluation of ligand-receptor binding free energies.
View Application Entry for Liaison

QSite is a new mixed mode QM/MM program for highly accurate energy calculations of protein-ligand interactions in the active site. The program is specifically designed for proteins and allows a number of different QM/MM boundaries for residues in the active site. QSite uses the power and speed of Jaguar to perform the quantum mechanical part of the calculations and OPLS-AA to perform the molecular mechanical part of the calculations.
View Application Entry for QSite

FlexX is a computer program for predicting protein-ligand interactions. For a protein with known three-dimensional structure and a small ligand molecule, FlexX predicts the geometry of the protein-ligand complex and estimates the binding affinity. The two main applications of FlexX are complex prediction and virtual screening. Complex prediction is used, when you have a protein and a small molecule binding to it but no structure of the protein-ligand complex. FlexX can be used to create and rank a series of possible protein-ligand complexes. In virtual screening, you have a protein and a set of compounds and you are interested in prioritizing the compounds for experimental testing.
View Application Entry for FlexX

LIGPLOT is a program for automatically plotting protein-ligand interactions and generating schematic diagrams of the interactions for a given PDB file.
View Application Entry for LIGPLOT

Situs is a program package for the docking of protein crystal structures to single-molecule, low-resolution maps from electron microscopy or small angle X-ray scattering.
View Application Entry for Situs

FlexiDock is a commercial software performs flexible docking of ligands into receptor binding sites. It is available for SGI R4000, 5000, 8000, 10000, 12000.
View Application Entry for FlexiDock

GRAMM is a free program for protein docking. To predict the structure of a complex, it requires only the atomic coordinates of the two molecules (no information about the binding sites is needed). The program performs an exhaustive 6-dimensional search through the relative translations and rotations of the molecules. The molecular pairs may be: two proteins, a protein and a smaller compound, two transmembrane helices, etc. GRAMM may be used for high-resolution molecules, for inaccurate structures (where only the gross structural features are known), in cases of large conformational changes, etc. GRAMM is compiled on SGI R10000, SGI R4000, SGI R4400, SGI R8000, Sun SPARC, IBM RS6000, DEC Alpha, and PC (Windows95 and Linux).
View Application Entry for GRAMM (Global RAnge Molecular Matching)

FTDock is a free program which performs rigid-body docking on two biomolecules in order to predict their correct binding geometry. FTDock outputs multiple predictions that can be screened using biochemical information. The software has been tested under SGI Irix versions 5.3, 6.2 and 6.5, and under RedHat Linux 6.2 (Linux 2.2.12) on Pentium-based platforms.
View Application Entry for FTDock (Fourier Transform Docking )

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. It is available for free for academics institutions and can be installed on most unix machines.
View Application Entry for AutoDock

DOCK is a software that can examine possible binding orientations of protein-protein and protein- DNA complexes. It can be used to search databases of molecular structures for compounds which act as enzyme inhibitors or which bind to target receptors. It can also search databases for DNA-binding compounds. It is available for unix workstations and is free for academic users.
View Application Entry for DOCK