BioTech FYI Center - Resources

Bioinformatic - Molecular Modeling Software Tools

  1. FTDock FTDock ( Fourier Transform Dock ) 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.beginners and experts. VigyaanCD i
  2. ArgusLab It is an incredible molecular modeling, graphics, and drug design program.
  3. Biodesigner It is a molecular modeling and visualization program for personal computers which is capable of creating homologous models of proteins, evaluate, and refine the models.
  4. Chem2Pac Chem2Pac is intended to be a kind of computational chemistry integrator, which has a multiple document interface, a molecular rendering utility, and allows the manipulation of various files.
  5. Cn3D Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.
  6. Dang Dang reads coordinates from a Protein DataBank (PDB) molecular structure file and generates a table of several useful geometric measurements for each residue or base. In its most basic form, it writes out dihedral angles (phi, psi, chi) hence the name. Th
  7. DomainFinder It is an interactive program for the determination and characterization of dynamical domains in proteins. Its key features are computational efficiency: even large proteins can be analyzed using a desk computer in a few minutes ease of use: a state-of-the
  8. Easy Winbabel It's a program for chemists and physicists dealing with molecular modeling. It uses the well known BABEL program as basis and provides a windows interface. The zip file includes BABEL ver 1.6.
  9. EDPDB EdPDB is a program to manipulate and extract information from Brookhaven Protein Databank (PDB) format coordinate file(s) of three-dimensional protein structures.
  10. Garlic It is a free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, unix, linux, free software download, open source software.
  11. Ghemical Ghemical is a computational chemistry software package released under the GNU GPL. Geometry optimization, molecular dynamics and some visualization tools are currently available. If quantum-mechanical calculations are needed, Ghemical can be directly link
  12. gOpenMol gOpenMol graphics interface to the OpenMol and can be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbital's, electron densities and electrostatic potentials.
  13. GRAMM GRAMM is a 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
  14. GROMACS GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
  15. Hex Hex is an interactive protein docking and molecular superposition program. Currently, Hex understands protein and DNA structures in PDB format.
  16. KineMage A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond immediately: the entire image can be rotated in real time, parts of the display can be turned on or off, p
  17. LOOPP LOOPP is a fold recognition program based on the collection of numerous signals, merging them into a single score, and generating atomic coordinates based on an alignment into a homologue template structure.
  18. MOIL MOIL is a molecular modeling software, which is in the public domain, and is written in the group of Ron Elber. Available features, such as energy calculations, minimization and calculations of classical trajectories. Graphic User Interface for a wide ran
  19. MOLMOL MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.
  20. Molscript A program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations
  21. NAMD 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 platfo
  22. NOC It is a free program for protein structure model-building, visualization, validation and analysis.
  23. Open Babel Open Babel is a project designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry.
  24. Rasmol Rasmol is a molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules.
  25. Raster3D Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficien
  26. Reduce Reduce is a program for adding hydrogens to a Protein Data Bank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. B
  27. Swiss-PdbViewer Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant
  28. Swiss-PdbViewer TraX (Trajectory eXplorer) is a simple Biodesigner-like program working under Linux and Windows. The program allows reading a protein folding simulation trajectory (TRA file) and saving a single frame as a PDB file.
  29. VEGA VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it's evolved to a complete molecular modeling suite.
Bioinformatic - Molecular Modeling Software Tools