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Molecular Distance Measures—a tutorial on how to calculate RMSD; RMSD—another tutorial on how to calculate RMSD with example code; Secondary Structure Matching (SSM) — a tool for protein structure comparison. Uses RMSD. GDT, LCS and LGA — different structure comparison measures. Description and services.
Free open source: ms-2.de: OpenMM: No No Yes Yes Yes Yes No Yes Yes High Performance MD, highly flexible, Python scriptable Free open source MIT: OpenMM: Orac: No No Yes Yes No Yes No Yes No Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level Free open source: Orac download page ...
The Molecular Modelling Toolkit (MMTK) is an open-source software package written in Python, which performs common tasks in molecular modelling. [1]The Molecular Modeling Toolkit is a library that implements common molecular simulation techniques, with an emphasis on biomolecular simulations.
Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. [3] VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge. [4]
In bioinformatics, the root mean square deviation of atomic positions is the measure of the average distance between the atoms of superimposed proteins. In structure based drug design, the RMSD is a measure of the difference between a crystal conformation of the ligand conformation and a docking prediction.
This free software had an earlier incarnation, Macsyma. Developed by Massachusetts Institute of Technology in the 1960s, it was maintained by William Schelter from 1982 to 2001. In 1998, Schelter obtained permission to release Maxima as open-source software under the GNU General Public license and the source code was released later that year ...
A free PyMol plugin easily implementing Kabsch is . (This previously linked to CEalign , but this uses the Combinatorial Extension (CE) algorithm.) VMD uses the Kabsch algorithm for its alignment. The FoldX modeling toolsuite incorporates the Kabsch algorithm to measure RMSD between Wild Type and Mutated protein structures.
The TM-score is intended as a more accurate measure of the global similarity of full-length protein structures than the often used RMSD measure. The TM-score indicates the similarity between two structures by a score between ( 0 , 1 ] {\displaystyle (0,1]} , where 1 indicates a perfect match between two structures (thus the higher the better ...