Constructing lattice models of protein chains with side groups

B A Reva; D S Rykunov; A J Olson; A V Finkelstein

doi:10.1089/cmb.1995.2.527

Constructing lattice models of protein chains with side groups

J Comput Biol. 1995 Winter;2(4):527-35. doi: 10.1089/cmb.1995.2.527.

Authors

B A Reva¹, D S Rykunov, A J Olson, A V Finkelstein

Affiliation

¹ Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.

PMID: 8634904
DOI: 10.1089/cmb.1995.2.527

Abstract

An algorithm to construct lattice models of polymers with side chains is presented. A search for the global minimum of the error function for a given lattice-to-chain orientation is done by dynamic programming, making the search both fast and complete. Application of the algorithm is illustrated by constructing lattice models for 12 proteins of different sizes and structural types.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, P.H.S.

MeSH terms

Algorithms*
Animals
Models, Molecular*
Molecular Structure
Protein Conformation
Protein Structure, Secondary
Proteins / chemistry*

Substances

Proteins

Grants and funding

P01GM38794/GM/NIGMS NIH HHS/United States