Dear all, Suppose I want to data mine the PDB to find a set of structures containing a motif that is characterized by an unusual conformation of backbone atoms over a short stretch of residues. This structural motif does not correspond to any specific amino acid sequence; the residues could be anything, as long as they conform to the right backbone conformation, within an RMSD of 1 angstrom or so. I then want to filter the list of "hits" with a solvent accessibility criterion, and then with a sequence criterion at one amino acid position within the motif.
This project is similar to one described previously by Richard Jackson and Robert Russell in J Mol Biol (2000) 296, 325-334. They wrote "The coordinates of a probe structure are compared to each segment of the same length within representatives from the SCOP database. Secondary structure assignments were taken from the DSSP database, and relative solvent accessibilities calculated using NACCESS." For a person without prior experience in data mining structural databases, where would be a good place to start? Can this type of search be done through a web server? What current software is best suited for the job? Are there any with user-friendly interfaces, helpful tutorials, and the like? Thanks for any suggestions. Evette Evette S. Radisky, Ph.D. Assistant Professor Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372 (office) (904) 953-0046 (lab)
