Automated main-chain model building by template matching and iterative fragment extension

Abstract

An algorithm for the automated macromolecular model building of polypeptide backbones is described. The procedure is hierarchical. In the initial stages, many overlapping polypeptide fragments are built. In subsequent stages, the fragments are extended and then connected. Identification of the locations of helical and beta-strand regions is carried out by FFT-based template matching. Fragment libraries of helices and beta-strands from refined protein structures are then positioned at the potential locations of helices and strands and the longest segments that fit the electron-density map are chosen. The helices and strands are then extended using fragment libraries consisting of sequences three amino acids long derived from refined protein structures. The resulting segments of polypeptide chain are then connected by choosing those which overlap at two or more C(alpha) positions. The fully automated procedure has been implemented in RESOLVE and is capable of model building at resolutions as low as 3.5 A. The algorithm is useful for building a preliminary main-chain model that can serve as a basis for refinement and side-chain addition.

Cited by papers we hold 4

• An introduction to experimental phasing of macromolecules illustrated by SHELX ; new autotracing features · 2018
  No notice
• Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation · 2015
  No notice
• PHENIX : a comprehensive Python-based system for macromolecular structure solution · 2010
  No notice
• Experimental phasing with SHELXC / D / E : combining chain tracing with density modification · 2010
  No notice

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.