PROSPECT Version 2.0: Introduction Installation Quick Guide Running Prospect Manager Input Formats Templates Parameters Configurations Outputs References FAQ

Mutation Energy Mutation energy describes the compatibility of substituting one amino acid by another in evolution. PROSPECT uses the PAM250 substitution matrix (data/parameters/gonnet.param) by default.  If 'freq file' is used, a profile-profile mutation energy replaces the PAM250 substitution matrix. Singleton Energy Singleton energy represents a residue's local preference of secondary structures (helix, sheet, or loop) and its preference for a certain solvent environment (exposed to solvent or in the interior of the protein). The singleton energy parameters used by PROSPECT (data/parameters/singleton.param) are derived from the FSSP database of unique protein structures. Pairwise Energy Pairwise energy describes the preference of a pair of amino acid types to be closer than a certain distance cutoff.  PROSPECT has two types of pairwise energy parameter sets; distance-dependent (data/parameters/pairwise_d5.param, etc) and distance-independent (data/parameters/pairwise.param)  The default pairwise energy used by PROSPECT 1 is distance-independent, and its cutoff distance is 7A.  PROSPECT 2 uses a distance-depenedent pairwise energy parameters. Only the pairwise interactions between core residues are taken into account. The pairwise energy parameters used by PROSPECT are derived from the FSSP database of unique protein structures. Gap Penalty PROSPECT uses a linear gap penalty function to penalize the length difference between a loop in a structural template and its aligned (loop) region in the query sequence. The open gap penalty is 10.8 and each elongation penalty is 0.6 by default.