Coarse-grained protein models and their applications

S Kmiecik, D Gront, M Kolinski, L Wieteska… - Chemical …, 2016‏ - ACS Publications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

Theory of protein folding: the energy landscape perspective

JN Onuchic, Z Luthey-Schulten… - Annual review of …, 1997‏ - annualreviews.org
▪ Abstract The energy landscape theory of protein folding is a statistical description of a
protein's potential surface. It assumes that folding occurs through organizing an ensemble of …

Funnels, pathways, and the energy landscape of protein folding: a synthesis

JD Bryngelson, JN Onuchic, ND Socci… - Proteins: Structure …, 1995‏ - Wiley Online Library
The understanding, and even the description of protein folding is impeded by the complexity
of the process. Much of this complexity can be described and understood by taking a …

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

KT Simons, C Kooperberg, E Huang, D Baker - Journal of molecular biology, 1997‏ - Elsevier
We explore the ability of a simple simulated annealing procedure to assemble native-like
structures from fragments of unrelated protein structures with similar local sequences using …

Evaluation of comparative protein modeling by MODELLER

A Šali, L Potterton, F Yuan… - Proteins: structure …, 1995‏ - Wiley Online Library
We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic
acid binding protein I, and human eosinophil neurotoxin that were calculated by Modeller, a …

The protein folding 'speed limit'

J Kubelka, J Hofrichter, WA Eaton - Current opinion in structural biology, 2004‏ - Elsevier
How fast can a protein possibly fold? This question has stimulated experimentalists to seek
fast folding proteins and to engineer them to fold even faster. Proteins folding at or near the …

Protein-folding dynamics: overview of molecular simulation techniques

HA Scheraga, M Khalili, A Liwo - Annu. Rev. Phys. Chem., 2007‏ - annualreviews.org
Molecular dynamics (MD) is an invaluable tool with which to study protein folding in silico.
Although just a few years ago the dynamic behavior of a protein molecule could be …

[PDF][PDF] Protein modeling and structure prediction with a reduced representation.

A Kolinski - Acta Biochimica Polonica, 2004‏ - frontierspartnerships.org
Protein modeling could be done on various levels of structural details, from simplified lattice
or continuous representations, through high resolution reduced models, employing the …

Advances in comparative protein-structure modelling

R Sanchez, A Šali - Current opinion in structural biology, 1997‏ - Elsevier
Comparative modelling of protein 3D structure can now be applied with reasonable
accuracy to ten times more protein sequences than the number of experimentally …

Ab initio protein structure prediction: progress and prospects

R Bonneau, D Baker - Annual review of biophysics and …, 2001‏ - annualreviews.org
▪ Abstract Considerable recent progress has been made in the field of ab initio protein
structure prediction, as witnessed by the third Critical Assessment of Structure Prediction …