Computational Chemistry

SBGrid supports 20 computational chemistry software titles. The following software packages are supported by SBGrid; availability of a specific software package may be limited based on license requirements.

Software Title Description Linux 32-bit Linux 64-bit OS X Intel Links

AutoDock

- 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 a known 3D structure.

yes yes yes

AutoDock Vina

- an open-source program for drug discovery, molecular docking, and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.

yes yes yes

CONCOORD

- a method to generate protein conformations around a known structure based on geometric restrictions.

yes yes yes

DOCK

- a molecular docking application that can be used to a) predict binding modes of small molecule-protein complexes; b)search databases of ligands for compounds that inhibit enzyme activity; c) search databases of ligands for compounds that bind a particular protein; d) search databases of ligands for compounds that bind nucleic acid targets; e) examine possible binding orientations of protein-protein and protein-DNA complexes; f) help guide synthetic efforts by examining small molecules that are computationally derivatized. A recent publication (see citations) describes how DOCK can be used to model RNA--small molecule complexes.

yes yes yes

GROMACS

- a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids. GROMACS was first developed in Herman Berendsens group, department of Biophysical Chemistry of Groningen University. It is a team effort, which is currently lead by Erik Lindahl, David van der Spoel and Berk Hess. GROMACS offers a user friendly interface and provides high performance.

yes yes yes

HADDOCK

- (High Ambiguity Driven biomolecular DOCKing) relies on an approach that makes use of biochemical and/or biophysical interaction data, such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions. HADDOCK was written by Alexandre Bondvin is derived from ARIA scripts by Michael Nilges and Jens Linge.

yes yes yes

Integrative Modeling Platform (IMP)

- is designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.

yes yes yes

MODELLER

- is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. A graphical interface to MODELLER is commercially available from Accelrys, as part of Discovery Studio Modeling 1.1.

yes yes yes

NAMD

- a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

yes yes yes

PROSPECT

- a threading-based protein structure prediction system.

yes yes

PyRosetta

- an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.

yes yes yes

Rosetta

- a software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. ROSETTA has been consistently successful in CASP and CAPRI competitions. Rosetta is also used for improving NMR and homology models before they are used in molecular replacement. Application developed and maintained by Baker Laboratory at the University of Washington.

yes yes yes

Schrodinger Suite

A suite of tools for small molecule drug discovery. The Schrodinger Suite runs on Linux and Mac workstations, but due to it’s size, it is not included in our default installation. To add Schrördinger to your installation, please email <bugs@sbgrid.org>.

yes yes yes

SCWRL3

- program for prediction of protein side-chain conformations.

yes yes

SCWRL4

- program for prediction of protein side-chain conformations.

yes yes yes

Solvate

- a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations. Solvate generates irregularly-shaped solvent volumes, adapted to a given solute's structure; allows efficient computation of boundary forces as required in molecular dynamics simulations; guarantees a minimal solute-boundary-distance; allows to specify a minimum solvent surface curvature in order to avoid `flat' surface regions; generates `disordered' (= fluid) water, not a grid of water molecules (= ice); locally minimizes the positions of all water molecules; optionally places salt ions obeying a Debye-Hückel distribution; optionally places (and marks) buried water molecules; and is X-PLOR/CHARMm-compatible, i.e., input and output is in pdb-/psf-format.

yes yes yes

THREADER

- offers protein fold recognition by optimal protein sequence threading.

yes yes

YUP

- (Yammp Under Python) a molecular modeling program designed as a general purpose tool, although development is currently concentrated on molecular simulations (mechanics) and on reduced representation and multiscale modeling. YUP is based on an earlier program Yammp. Also known as Yammp 2.

yes yes yes

ZDOCK/RDOCK

- two protein docking algorithms designed to operate in succession. ZDOCK is a rigid-body docking program, and RDOCK is a refinement program. ZDOCK uses a fast Fourier transform to search all possible binding modes for 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. From the Zhiping Lab at Boston University. by RDOCK.

yes yes yes

ZINC

a free database of commercially-available compounds for virtual screening. ZINC contains over 21 million purchasable compounds in ready-to-dock, 3D formats. ZINC is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). To cite ZINC, please reference: Irwin, Sterling, Mysinger, Bolstad and Coleman, J. Chem. Inf. Model. 2012 DOI: 10.1021/ci3001277. The original publication is Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82 PDF, DOI. We thank NIGMS for financial support (GM71896).