VESTA (Visualization System for Electronic & Structural Analysis) is a 3D visualization program for structural models and 3D grid data such as electron/nuclear densities. Some of the novel features of VESTA are listed below.
AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.
Gromita is a Graphical User Interface (GUI) for GROMACS (v.3 and 4). It is writen in perl making extensive use of perl/tk achieving portability in a wide variety of operating systems and architectures. Gromita provides friendly to use buttons in a windows-based environment while maintaining a terminal mode for the experienced user.
ArgusLab is a molecular modeling, graphics, and drug design program.The ArgusDock docking engine, implemented in ArgusLab4.0, approximates an exhaustive search method, with similarities to DOCK and Glide. Flexible ligand docking is possible with ArgusLab, where the ligand is described as a torsion tree and grids are constructed that overlay the binding site. Ligand’s root node (group of bonded atoms that do not have rotatable bonds) is placed on a search point in the binding site and a set of diverse and energetically favorable rotations is created. For each rotation, torsions in breadth-first order are constructed and those poses that survive the torsion search are scored. The N-lowest energy poses are retained and the final set of poses undergoes coarse minimization, re-clustering and ranking.
Thompson, M. A. (2004).
Molecular docking using ArgusLab, an efficient shape-based search algorithm and the AScore scoring function.
ACS meeting, Philadelphia, 172, CINF 42, PA.
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.
Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, and David E. Shaw,
“Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters,”
Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17, 2006
p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files).
TuftsViewer is an open source program that allows the visualization, rotation and coordinated viewing of multiple 3D protein molecules on the 2D screen.
TuftsViewer has been renamed to Molli. Molli is an open source cross-platform protein structure viewer based on the OpenGL and wxWidgets libraries.
pdbTools is a set of command line python scripts that manipulate wwPDB protein and nucleic acid structure files. There are many programs, both open source and proprietary, that perform similar tasks; however, most of these tools are buried within programs of larger functionality.
