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Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
Comprehensive life science modeling and simulation suite of applications focused on optimizing drug discovery process: small molecule simulations, QM-MM, pharmacophore modeling, QSAR, protein-ligand docking, protein homology modeling, sequence analysis, protein-protein docking, antibody modeling, etc. Proprietary, trial available
RaptorX is a software and web server for protein structure and function prediction that is free for non-commercial use. RaptorX is among the most popular methods for protein structure prediction. RaptorX is among the most popular methods for protein structure prediction.
Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). [2] [3] It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins (protein NMR), termed satisfaction of spatial restraints, by which a set of geometrical criteria are used to create a probability ...
GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids.It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide.
Coot is free software, distributed under the GNU GPL. It is available from the Coot web site [ 4 ] originally at the University of York , and now at the MRC Laboratory of Molecular Biology . Pre-compiled binaries are also available for Linux and Windows from the web page and CCP4 , and for Mac OS X through Fink and CCP4.
Build, edit and visualise small molecules, macromolecules, protein-ligand complexes, crystal lattices, molecular and property surfaces. Platform for extensive collection of molecular modelling / drug discovery applications. Molekel: MM XRD: Free open-source: Java 3D applet or standalone program: Ovito: MM XRD EM MD: Free open-source: Python [13 ...
MassMatrix is a database search algorithm for tandem mass spectrometric data. It uses a mass accuracy-sensitive, probabilistic scoring model to rank peptide and protein matches. MassWiz Open source: MassWiz is a search algorithm developed at the Institute of Genomics and Integrative Biology that can be used as a Windows command-line tool.