Recognition of remote protein homologies using three-dimensional information to generate a position specific scoring matrix in the program 3D-PSSM

A method (3D-PSSM) to recognise remote protein sequence homologues is described.The method uses homologous proteins of similar three-dimensional structure in the SCOP database (Murzin, A. G. et al., 1995, J. Mol.Biol.247, 536-540) to obtain a structural equivalence of residues.These equivalences are used to extend multiply-aligned sequences obtained by standard sequence searches (i.e.lDprofiles).The resultant 3D profile is converted into a position specific scoring matrix (a 3D-PSSM).The approach is benchmarked on recognising remote homologues in the SCOP database and comparing the hit and error rates.3D-PSSMs are compared with lD-PSSMs and with two widely-used sensitive search approaches -PSI-BLAST (Altschul, S.