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Name Description Links
a heavily optimized molecular dynamics (MD) engine specially designed to run on NVIDA GPUs. It is extremely fast (115ns/day for DHFR using 1 GPU) and performs MD simulations on the microsecond scale in a single workstation. ACDMD can read CHARMM/NAMD and AMBER input files, works with CUDA and OpenCL, and uses similar syntax to other MD software.

Restriction: available to nonprofit users who register using the htmd_register command.

consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models
a "pipeline" for processing and analysis of EM images. Appion consists of a web-based user interface linked to a set of python scripts that control several underlying integrated processing packages. All data input and output within Appion is managed using tightly integrated SQL databases.
a suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of a known 3D structure.
a program for drug discovery, molecular docking, and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.
an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
a method to generate protein conformations around a known structure based on geometric restrictions.
a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods, and classical force fields.
a program for calculating protein electrostatics.

Restriction: available to nonprofit users who register with Columbia & submit confirmation to SBGrid.

a molecular docking application used to a) predict binding modes of small molecule-protein complexes; b) search databases of ligands for compounds that inhibit enzyme activity, bind a particular protein, bind nucleic acid targets; c) examine possible binding orientations of protein-protein and protein-DNA complexes; d) help guide synthetic efforts by examining small molecules that are computationally derivatized. Dock is offered in the SBGrid collection in ...
a software package designed for the numerical solution of the Poisson-Boltzmann equation (PBE). This software was written by Nathan Baker in collaboration with J. Andrew McCammon and Michael Holst and enhanced by several others.
(Fast Rotational DOCKing) a tool used to efficiently generate many potential predictions of how two proteins could interact.
a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.
(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.
computes the hydrodynamic properties of rigid macromolecules (proteins, small nucleic acids, macromolecular complexes, etc.) from their structure, as specified by the coordinates taken from a PDB file supplied by the user, from which the proper hydrodynamic model is built by the program itself.
a toolkit to perform Normal Mode Analysis (NMA) in internal coordinates (IC) on both protein and nucleic acid atomic structures. Vibrational analysis, motion animations, morphing trajectories and Monte-Carlo simulations can be easily carried out at different scales of resolution using this toolkit.
(Integrative Modeling Platform) designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.
(Multi-Conformation Continuum Electrostatics) a biophysics simulation program combining continuum electrostatics and molecular mechanics. In this program, the protein side chain motions are simulated explicitly while the dielectric effect of solvent and bulk protein material is modeled by continuum electrostatics.
an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.
a program that is used for including solvation effects in biological systems, such as proteins, using an atomic model of the protein. This is done by solving the Poisson-Boltzmann equation in a dielectric medium, including distributed point charges on a grid.
a software package for visualization and analysis of molecular structures comprising AutoDockTools (ADT): a graphical front-end for setting up and running AutoDock; Python Molecule Viewer (PMV); and Vision: a visual-programming environment for building networks describing novel combinations of computational methods and yielding new visualizations of their data.
a series of software tools for docking flexible ligands into receptors with selective flexibility, comprising: 1) AutoDockFR: a docking engine using the AutoDock4 forcefield; 2) AutoGridFR: a graphical user interface for setting up docking boxes; 3) AutoSite: a ligand binding site detection and characterization program.
(Metropolis Monte Carlo) a program for the simulation of molecular assemblies in the canonical, grand-canonical and isothermal-isobaric ensembles employing several convergence acceleration techniques (e.g., force-biased displacement, extension-biased and local torsion changes, preferential selection of solvent to be moved, cavity-biased insertion, virial-biased volume change).
(Multiscale Modeling Tools for Structural Biology) a collection of perl-based user-level utilities as well as programming libraries for multiscale protein structure modeling. Intended applications include protein structure prediction, loop modeling, structure refinement, and structure evaluation/scoring.
used for homology or comparative modeling of protein three-dimensional structures. From a sequence alignment with known related structures MODELLER automatically calculates a model containing all non-hydrogen atoms using comparative protein structure modeling by satisfaction of spatial restraints. It can also perform de novo modeling of loops in protein structures, optimize various models of protein structure with respect to a flexibly defined objective function, multiple ...
a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
a high performance toolkit for molecular simulation that can be used either as a stand-alone application for running simulations or as a library you call from your own code.
an electronic structure program package that is a flexible, efficient, and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.
a Python package that automates structure preparation tasks for continuum electrostatics calculations. It can convert protein files in PDB format to PQR format. It can add a limited number of missing heavy atoms to biomolecular structures, determine side-chain pKas, placing missing hydrogens, optimize the protein for favorable hydrogen bonding, and assign charge and radius parameters from a variety of force fields.
an easy to use application that fixes problems in Protein Data Bank files in preparation for simulating. Fixes include: adding missing heavy or hydrogen atoms, building missing loops, convert non-standard residues to their standard equivalents, deleting unwanted heterogens or chains from the model, and building a water box for explicit solvent simulations.
a linear-scaling, semiempirical quantum mechanics (SE-QM) program DivCon with the Phenix X-ray refinement engine. Phenix/DivCon does not utilize CIF(s), link restraints and other refinement parameters so there are fewer assumptions about the model. Accurate energy and density scoring tools also allow tautomer/protomer and “flip state” determination.
an open source library for free energy calculations in molecular systems that works with some of the most popular molecular dynamics engines. Perform free energy calculations as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation-based steered MD.
a protein structural dynamics analysis software package. ProDy is installed as a module within python.
a threading-based protein structure prediction system.
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.
a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.
a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.
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.

Restriction: basic access available to non-profit users in North America and Australia.

a program for prediction of protein side-chain conformations.
a program for prediction of protein side-chain conformations.
a collection of utilities designed to help setting up and analyze molecular simulations.
A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.
a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations.
a parallel molecular docking program that is a modified version of the very popular PC-based molecular docking program AutoDock Vina. VinaLC is a message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines.
a combination of the X-PLOR structure determination program and VMD (Visual Molecular Dynamics) - a freely available molecular visualization program. This package allows manual manipulation of the protein structures to satisfy experimental NMR data, and can also be used to visualize the goodness of fit of a particular model to given restraints.

Restriction: available to users who register with the NIH & submit confirmation to SBGrid.

(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.
a full rigid-body search of docking orientations between two proteins.
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).
a subset of chemical compounds that are used for screening at the ICCB-Longwood Screening Facility. The dataset was compiled by David Wrobel (ICCB-Longwood) for in silico docking. The date-stamped datasets are available in /programs/share/iccb.
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