ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.

ABSTRACT: Assessing structural similarity and defining common regions through comparison of protein spatial structures is an important task in functional and evolutionary studies of proteins. There are many servers that compare structures and define sub-structures in common between proteins through superposition and closeness of either coordinates or contacts. However, a natural way to analyze a structure for experts working on structure classification is to look for specific three-dimensional (3D) motifs and patterns instead of finding common features in two proteins. Such motifs can be described by the architecture and topology of major secondary structural elements (SSEs) without consideration of subtle differences in 3D coordinates. Despite the importance of motif-based structure searches, curre

SUBMITTER: Shi S 

PROVIDER: S-EPMC2703969 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature