Example M3R-PDB output.
M3R-PDB program (Missense Mutation Mapper and Randomizer for PDB files) is a cross-platform solution written in Python 2 programming language, which facilitates the process of generation of computer models of proteins with somatic mutations. The program expects the following input arguments: 1) the name of a gene to search missense mutations of; 2) the name of a PDB file of a source isoform model encoded by the gene specified; 3) the number of models to generate, with each of them bearing exactly one randomly chosen missense mutation. M3R-PDB solves the problem automatically in several steps. The first step is the connection to the somatic mutations database COSMIC and fetching a list of missense mutations for the gene specified, including histological information. The second step is the connection to the NCBI database to fetch a list of known isoforms of the enzyme, including their FASTA sequences. Then the program searches for the isoform which COSMIC mutations are mapped to, by comparing positions of the mutations with the sequences of the isoforms. Finally, M3R-PDB picks the mutations that can be introduced in the source PDB model (source aminoacid residues match), randomly chooses the certain number of mutations and writes a set of PDB files; each of the output files bears one chosen missense mutation.
MDCrd2PDBS program is an utility which converts trajectories in AMBER format to a set of PDB files. It simultaneously solves the problem of picking only a small set of relevant water molecules instead of the whole water box. The program will keep only those solvent molecules which meet a certain condition (proximity to a certain residue during certain amount of time), and is also able to process incomplete trajectories. In particular, one can use it to get preliminary data while production MD is still running.
Both programs are freely available under the terms of GNU GPL.
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