Simulating protein evolution in sequence and structure space
Naturally occurring proteins comprise a special subset of all plausible sequences and
structures selected through evolution. Simulating protein evolution with simplified and all …
structures selected through evolution. Simulating protein evolution with simplified and all …
The structure of protein evolution and the evolution of protein structure
RA Goldstein - Current opinion in structural biology, 2008 - Elsevier
The observed distribution of protein structures can give us important clues about the
underlying evolutionary process, imposing important constraints on possible models. The …
underlying evolutionary process, imposing important constraints on possible models. The …
Functionality and the evolution of marginal stability in proteins: inferences from lattice simulations
PD Williams, DD Pollock… - Evolutionary …, 2006 - journals.sagepub.com
It has been known for some time that many proteins are marginally stable. This has inspired
several explanations. Having noted that the functionality of many enzymes is correlated with …
several explanations. Having noted that the functionality of many enzymes is correlated with …
Advances on protein folding simulations based on the lattice HP models with natural computing
X Zhao - Applied Soft Computing, 2008 - Elsevier
This paper introduces the hydrophobic-polar (HP) models and several natural computing
approaches. The biological background of the protein structure prediction, the Levinthal …
approaches. The biological background of the protein structure prediction, the Levinthal …
CPSP-tools–Exact and complete algorithms for high-throughput 3D lattice protein studies
Background The principles of protein folding and evolution pose problems of very high
inherent complexity. Often these problems are tackled using simplified protein models, eg …
inherent complexity. Often these problems are tackled using simplified protein models, eg …
Probing protein fold space with a simplified model
We probe the stability and near-native energy landscape of protein fold space using
powerful conformational sampling methods together with simple reduced models and …
powerful conformational sampling methods together with simple reduced models and …
A structure-centric view of protein evolution, design, and adaptation
EJ Deeds, EI Shakhnovich - … in Enzymology & Related Areas of …, 2007 - Wiley Online Library
A structure-centric view of protein evolution, design, and adaptation Page 148 A
STRUCTURE-CENTRIC VIEW OF PROTEIN EVOLUTION, DESIGN, AND ADAPTATION By …
STRUCTURE-CENTRIC VIEW OF PROTEIN EVOLUTION, DESIGN, AND ADAPTATION By …
Coupled folding–binding versus docking: A lattice model study
N Gupta, A Irbäck - The Journal of chemical physics, 2004 - pubs.aip.org
Using a simple hydrophobic/polar protein model, we perform a Monte Carlo study of the
thermodynamics and kinetics of binding to a target structure for two closely related …
thermodynamics and kinetics of binding to a target structure for two closely related …
Comparative modeling and protein‐like features of hydrophobic–polar models on a two‐dimensional lattice
S Moreno‐Hernández, M Levitt - Proteins: Structure, Function …, 2012 - Wiley Online Library
Lattice models of proteins have been extensively used to study protein thermodynamics,
folding dynamics, and evolution. Our study considers two different hydrophobic–polar (HP) …
folding dynamics, and evolution. Our study considers two different hydrophobic–polar (HP) …
Search strategies in structural bioinformatics
Optimisation problems pervade structural bioinformatics. In this review, we describe recent
work addressing a selection of bioinformatics challenges. We begin with a discussion of …
work addressing a selection of bioinformatics challenges. We begin with a discussion of …