TITLE

Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

AUTHOR(S)
Offman, Marc N.; Tournier, Alexander L.; Bates, Paul A.
PUB. DATE
January 2008
SOURCE
BMC Structural Biology;2008, Vol. 8, Special section p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Automatic protein modelling pipelines are becoming ever more accurate; this has come hand in hand with an increasingly complicated interplay between all components involved. Nevertheless, there are still potential improvements to be made in template selection, refinement and protein model selection. Results: In the context of an automatic modelling pipeline, we analysed each step separately, revealing several non-intuitive trends and explored a new strategy for protein conformation sampling using Genetic Algorithms (GA). We apply the concept of alternating evolutionary pressure (AEP), i.e. intermediate rounds within the GA runs where unrestrained, linear growth of the model populations is allowed. Conclusion: This approach improves the overall performance of the GA by allowing models to overcome local energy barriers. AEP enabled the selection of the best models in 40% of all targets; compared to 25% for a normal GA.
ACCESSION #
35702902

 

Related Articles

  • Are the same or different amino acid residues responsible for correct and incorrect protein folding? Galzitskaya, O. V. // Biochemistry (00062979);Feb2009, Vol. 74 Issue 2, p186 

    It has been shown for 20 proteins that amino acid residues included into the protein folding nucleus, determined experimentally, are often involved in the theoretically determined amyloidogenic fragments. For 18 proteins, Φ-values indicative of the extent of residue involvement into the...

  • Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure. Chakravarty, Suvobrata; Godbole, Sucheta; Bing Zhang; Berger, Seth; Sanchez, Roberto // BMC Structural Biology;2008, Vol. 8, Special section p1 

    Background: Although multiple templates are frequently used in comparative modeling, the effect of inclusion of additional template(s) on model accuracy (when compared to that of corresponding single-template based models) is not clear. To address this, we systematically analyze two-template...

  • FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking. Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam // Bioinformatics;Mar2014, Vol. 30 Issue 5, p660 

    Motivation: Homology detection enables grouping proteins into families and prediction of their structure and function. The range of application of homology-based predictions can be significantly extended by using sequence profiles and incorporation of local structural features. However,...

  • DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins. Wataru Nishima; Guoying Qi; Steven Hayward; Akio Kitao // Bioinformatics;Mar2009, Vol. 25 Issue 5, p628 

    Motivation: The biological function of proteins is associated with a variety of motions, ranging from global domain motion to local motion of side chain. We propose a method, dihedral transition analysis (DTA), to identify significant dihedral angle changes between two distinct protein...

  • Hidden conformations in protein structures. Ashkenazy, Haim; Unger, Ron; Kliger, Yossef // Bioinformatics;Jul2011, Vol. 27 Issue 14, p1941 

    Motivation: Prediction of interactions between protein residues (contact map prediction) can facilitate various aspects of 3D structure modeling. However, the accuracy of ab initio contact prediction is still limited. As structural genomics initiatives move ahead, solved structures of homologous...

  • Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case. García-Fandiño, Rebeca; Bernadó, Pau; Ayuso-Tejedor, Sara; Sancho, Javier; Orozco, Modesto // PLoS Computational Biology;Aug2012, Vol. 8 Issue 8, p1 

    The early stages of the thermal unfolding of apoflavodoxin have been determined by using atomistic multi microsecondscale molecular dynamics (MD) simulations complemented with a variety of experimental techniques. Results strongly suggest that the intermediate is reached very early in the...

  • Exploration of the relationship between topology and designability of conformations. Leelananda, Sumudu P.; Towfic, Fadi; Jernigan, Robert L.; Kloczkowski, Andrzej // Journal of Chemical Physics;6/21/2011, Vol. 134 Issue 23, p235101 

    Protein structures are evolutionarily more conserved than sequences, and sequences with very low sequence identity frequently share the same fold. This leads to the concept of protein designability. Some folds are more designable and lots of sequences can assume that fold. Elucidating the...

  • Statistical theory of neutral protein evolution by random site mutations. Bhattacherjee, Arnab; Biswas, Parbati // Journal of Chemical Sciences;Sep2009, Vol. 121 Issue 5, p887 

    Understanding the features of the protein conformational space represents a key component to characterize protein structural evolution at the molecular level. This problem is approached in a twofold manner; simple lattice models are used to represent protein structures with the ability of a...

  • A sequence-based hybrid predictor for identifying conformationally ambivalent regions in proteins. Yu-Cheng Liu; Meng-Han Yang; Win-Li Lin; Chien-Kang Huang; Yen-Jen Oyang // BMC Genomics;2009 Supplement 3, Vol. 10, Special section p1 

    Background: Proteins are dynamic macromolecules which may undergo conformational transitions upon changes in environment. As it has been observed in laboratories that protein flexibility is correlated to essential biological functions, scientists have been designing various types of predictors...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics