Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions

MSITE

a program designed to analyse structural data of liganded and unliganded proteins, written by Dr. Piotr Rotkiewicz in collaboration with Dr. Wanda Sicińska and Mateusz Kurciński.

MSITE is a simple command-line program for immediate identification of the nearest neighbors of a given amino acids (for example neighbors of residues that contact ligand or reorient their SC conformation in the presence of agonist/or antagonist) in any number of compared complexes. The arguments of the MSITE program are the names of protein structures (in PDB format) and a list of residues to be analyzed. The residues are listed individually for every input PDB structure. The program outputs a consensus list of residues being in contact with the residues specified in the input list. The contact is defined as a distance of 3.5 Angstroms or less between any pair of protons or heavy atoms of the contacting residues. The output list is divided and sorted according to the order of residues in the input list, thus allowing immediate identification and comparison of subtle structural differences between functionally important residues within a family of closely related structures.

To extract archive type:

gunzip msite.tar.gz

tar-xvf msite.tar

To compile MSITE program, use ANSI C compiler (e.g. GNU C):

cc msite.c -lm -o msite

To run msite, type:

./msite list.txt > output.txt

The program expects the input PDB files to be present in the working directory. Example input files are included in the program archive.