Protein decoy assembly using short fragments under geometric constraints
- 30 January 2003
- journal article
- Published by Wiley in Biopolymers
- Vol. 68 (3) , 278-285
- https://doi.org/10.1002/bip.10262
Abstract
A small set of protein fragments can represent adequately all known local protein structure. This set of fragments, along with a construction scheme that assembles these fragments into structures, defines a discrete (relatively small) conformation space, which approximates protein structures accurately. We generate protein decoys by sampling geometrically valid structures from this conformation space, biased by the secondary structure prediction for the protein. Unlike other methods, secondary structure prediction is the only protein‐specific information used for generating the decoys. Nevertheless, these decoys are qualitatively similar to those found by others. The method works well for all‐α proteins, and shows promising results for α and β proteins. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 278–285, 2003Keywords
This publication has 22 references indexed in Scilit:
- The birth of computational structural biology.Nature Structural & Molecular Biology, 2001
- Comparing search strategies for finding global optima on energy landscapesJournal of Computational Chemistry, 1999
- Ab Initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions 1 1Edited by F. CohenJournal of Molecular Biology, 1999
- Protein folding simulations with genetic algorithms and a detailed molecular descriptionJournal of Molecular Biology, 1997
- Principles of protein folding — A perspective from simple exact modelsProtein Science, 1995
- A test of lattice protein folding algorithms.Proceedings of the National Academy of Sciences, 1995
- A simple protein folding algorithm using a binary code and secondary structure constraintsProtein Engineering, Design and Selection, 1995
- A lattice model for protein structure prediction at low resolution.Proceedings of the National Academy of Sciences, 1992
- Consistent Force Field Calculations. II. Crystal Structures, Sublimation Energies, Molecular and Lattice Vibrations, Molecular Conformations, and Enthalpies of AlkanesThe Journal of Chemical Physics, 1970
- Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n-Alkane MoleculesThe Journal of Chemical Physics, 1968