Maxwell : Molecular Modeling and Dynamics

Created by Frank Schluenzen on Jan 13, 2022 09:47


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    arp_warp — ARP/wARP is a software suite to build macromolecular models in X-ray crystallography electron density maps. Structural genomics initiatives and the study of complex macromolecular assemblies and membrane proteins all rely on advanced methods for 3D structure determination.
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    autodock — 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. 
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    blast — The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
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    CMIstark — The Controlled Molecule Imaging group (CMI) at the Center for Free Electron Laser Science (CFEL) has developed the CMIstark  software to calculate, view, and analyze the energy levels of adiabatic Stark energy curves of linear, symmetric top and asymmetric top molecules. The program exploits the symmetry of the Hamiltonian to generate fully labeled adiabatic Stark energy curves.
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    fasta — The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
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    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. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
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    lammps — LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
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    namd — NAMD s a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. 
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    O — O is a graphical tool supporting 3D visualization for modeling 3D macromolecular structures into electron density maps. 
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    openbabel — Open Babel is a free, open-source version of the Babel chemistry file translation program. 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, computational chemistry, and many related areas.
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    vmd — VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. 
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    xcrysden — XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.