Modeling, docking, and dynamics
Resources
Babel is a program designed to interconvert a number of file formats currently used in molecular modeling.
http://smog.com/chem/babel/
The current version of Mol2Mol™ recognizes, reads and writes about 50 different file formats and subformats. It contains a simple graphic display module to inspect the currently loaded molecule. It possesses some chemical intelligence for recognizing detailed atom types, hybridization and chemical environments, which is necessary for converting simpler formats (like X-ray crystallographic files) to more advanced ones, or when hydrogen atoms are automatically to be added to the heavy atoms. Problematic files can be corrected within Mol2mol or as ASCII files by calling directly your favourite text editor.
http://web.interware.hu/frenzy/mol2mol/index.html
Remediator converts PDB files between PDBv2.3 and PDBv3.0 formats.
http://kinemage.biochem.duke.edu/software/remediator.php
Modeling & dyamics
"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. The current version of the code is Amber version 10, which is distributed by UCSF subject to a licensing agreement
http://ambermd.org/
AmberTools consists of several independently developed packages: nucleic acid builder (NAB), antechamber, ptraj, tleap and xleap, sleap.
http://ambermd.org/#AmberTools
Generation of Models for "Unusual" DNA and RNA
http://www.scripps.edu/mb/case/casegr-sh-3.2.html
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
http://www.cgl.ucsf.edu/chimera/
MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). 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.
http://salilab.org/modeller/modeller.html
The program TRITON is a graphical tool for computational aided protein engineering. It implements methodology of computational site-directed mutagenesis to design new protein mutants with required properties. It uses the external program MODELLER to model structures of new protein mutants based on the wild-type structure by homology modelling method. Subsequently, properties of these protein mutants are modelled.
http://ncbr.chemi.muni.cz/triton/triton.html
SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists World Wide.
http://swissmodel.expasy.org/SWISS-MODEL.html
YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux and Mac OS X developed since 1993, that finally makes it really easy to answer your questions.
http://www.yasara.org/
BALLView is a standalone molecular modeling and visualization application. It is also a framework for developing molecular visualization functionality. It is available free of charge under the GPL for Linux, Windows and MacOS.
http://www.ballview.org/
Visualization of molecular modelling.
http://www.eyesopen.com/products/applications/vida-vivant.html
Sirius is a component-based visualization framework designed for application in molecular modeling, drug discovery, protein structure analysis, as well as database mining and sequence-based work. It is equally suited for protein and small molecule construction and visualization.
http://sirius.sdsc.edu/
ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. Paritally free.
http://www.zmmsoft.com/
GROMACS: a suite for fast, free and flexible molecular dynamics (for advanced users)
http://www.gromacs.org
ModLoop is a web server for automated modeling of loops in protein structures. The server relies on the loop modeling routine in MODELLER that predicts the loop conformations by satisfaction of spatial restraints, without relying on a database of known protein structures.
http://modbase.compbio.ucsf.edu/modloop/modloop.html
A Server for Protein Structure Modeling
http://modbase.compbio.ucsf.edu/ModWeb20-html/modweb.html
The SALIGN webserver is still being tested, and is not yet ready for public use. Please check back again later, or use the equivalent functionality in the MODELLER program.
http://salilab.org/salign/
A Multi-platform 3D Stereo Molecular Dynamics Trajectory Visualization Package
http://structbio.vanderbilt.edu/~cmoth/mddisplay/
R.E.D. allows computational biologists involved in AMBER/GAFF, CHARMM, GLYCAM & OPLS force field based biological studies to derive atomic charge values of high quality and reproducibility, and to create force field libraries for new molecules and molecular fragments
http://q4md-forcefieldtools.org/RED/
H++ is an automated system that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H++ outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools useful for analysis of electrostatic-related molecular properties.
http://biophysics.cs.vt.edu/H++/
LOOS is a lightweight yet powerful and easy to use C++ library for structural analysis, geared primarily towards molecular dynamics simulations.
http://membrane.urmc.rochester.edu/Software/LOOS/LOOS.html
CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular dynamics and mechanics. It performs standard molecular dynamics in many different ensembles (e.g., NVE, NVT, NPT) using state-of-the-art algorithms for timestepping, long range force calculation and periodic images. CHARMM can be used for energy minimization, normal modes and crystal optimizations as well. The potential energy functions available for use with CHARMM have been extensively parameterized for simulations of proteins, nucleic acids and lipids.
http://www.charmm.org/
Yammp Under Python (YUP), also known as Yammp 2, is a molecular modeling program. Although a general purpose tool, development is currently concentrated on molecular simulations (mechanics) and on reduced representation and multiscale modeling. YUP is based on an earlier program Yammp.
http://rumour.biology.gatech.edu/YammpWeb/
Situs is an award-winning program package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering.
http://situs.biomachina.org/
Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry.
http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
A freely-license molecular modeling, graphics, and drug design program
http://www.arguslab.com/
The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
http://dasher.wustl.edu/tinker/
AMMP is a molecular mechanics and dynamics program. AMMP is a fully featured molecular modeling program.
http://www.cs.gsu.edu/~cscrwh/progs/progs.html
Jackal is a collection of programs designed for the modeling and analysis of protein structures.
http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Jackal
INTERCHEM is a general purpose molecular modelling program written by Robin Breckenridge and Peter Bladon of the University of Strathclyde.
http://www.interprobe.co.uk/inter/interchem.html
3D-Graphics program for Molecular Modeling and Visualization of Quantum Chemical Calculations
http://www1.bbiq.jp/zzzfelis/Facio.html
The Collaborative Computational Project Number 4 in Protein Crystallography was set up in 1979 to support collaboration between researchers working on such software in the UK, and to assemble a comprehensive collection of software to satisfy the computational requirements of the relevant UK groups. CCP4 was originally supported by the UK Science and Engineering Research Council (SERC), and is now supported by the Biotechnology and Biological Sciences Research Council (BBSRC).
http://www.ccp4.ac.uk
NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD and VMD for biomolecular modeling.
http://www.ks.uiuc.edu/Research/namd/
Docking
UCSF DOCK is a program for finding and optimizing the structures of small molecules in protein or nucleic acid receptor sites.
http://dock.compbio.ucsf.edu/
AstexViewer™ is a Java molecular graphics program that assists in structure based drug design.
http://www.astex-therapeutics.com/AstexViewer/index.php
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
http://www.cgl.ucsf.edu/chimera/
MGLTools is a software developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures. AutoDock is an automated docking software designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. PMV is a powerful molecular viewer that has a number of customizable features and comes with many pluggable commands ranging from displaying molecular surfaces to advanced volume rendering. Vision is a visual-programming environment in which a user can interactively build networks describing novel combinations of computational methods, and yielding new visualizations of their data without actually writing code.
http://mgltools.scripps.edu/
Sculptor is an interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures. We are developing Sculptor as a GUI-based extension of the Situs docking programs, to allow an interactive exploration and analysis of volumetric maps. Sculptor combines 3D rendering with advanced mathematical concepts like clustering techniques and pattern matching algorithms to permit an almost instantaneous fitting of the high-resolution structures and to facilitate typical post-processing work like map editing or resolution adjustment.
http://sculptor.biomachina.org/
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.
http://autodock.scripps.edu/
ESCHER Next Generation (NG) is an enhanced version of the original ESCHER protein-protein automatic docking system developed in 1997 by Gabriele Ausiello, Gianni Cesareni and Manuela Helmer Citterich.
http://users.unimi.it/%7Eddl/escherng/index.htm
Protein-Protein Docking Web Server for ranking of receptor-ligand complexes using energy filtering and clustering
http://nrc.bu.edu/cluster/
This is the Web interface to our current protein docking software made available to the public. This software is different from the original GRAMM, except that both packages use FFT for the global search of the best rigid body conformations.
http://vakser.bioinformatics.ku.edu/resources/gramm/grammx/