scholarly journals Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models

2014 ◽  
Vol 82 (7) ◽  
pp. 1549-1549
Author(s):  
Gniewek Pawel ◽  
Sumudu P. Leelananda ◽  
Kolinski Andrzej ◽  
Robert L. Jernigan ◽  
Kloczkowski Andrzej
Keyword(s):  
Quality Assessment ◽  
Coarse Grained ◽  
Native Structure ◽  
Structure Recognition ◽  
Protein Models

scholarly journals Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models

2011 ◽  
Vol 79 (6) ◽  
pp. 1923-1929 ◽  
Author(s):  
Pawel Gniewek ◽  
Sumudu P. Leelananda ◽  
Andrzej Kolinski ◽  
Robert L. Jernigan ◽  
Andrzej Kloczkowski
Keyword(s):  
Quality Assessment ◽  
Coarse Grained ◽  
Native Structure ◽  
Structure Recognition ◽  
Protein Models

scholarly journals Smooth orientation-dependent scoring function for coarse-grained protein quality assessment

2018 ◽  
Vol 35 (16) ◽  
pp. 2801-2808 ◽  
Author(s):  
Mikhail Karasikov ◽  
Guillaume Pagès ◽  
Sergei Grudinin
Keyword(s):  
Quality Assessment ◽  
Structure Prediction ◽  
High Performance ◽  
Protein Quality ◽  
Scoring Function ◽  
Structural Features ◽  
Coarse Grained ◽  
Supplementary Information ◽  
Single Model ◽  
Protein Models

Abstract Motivation Protein quality assessment (QA) is a crucial element of protein structure prediction, a fundamental and yet open problem in structural bioinformatics. QA aims at ranking predicted protein models to select the best candidates. The assessment can be performed based either on a single model or on a consensus derived from an ensemble of models. The latter strategy can yield very high performance but substantially depends on the pool of available candidate models, which limits its applicability. Hence, single-model QA methods remain an important research target, also because they can assist the sampling of candidate models. Results We present a novel single-model QA method called SBROD. The SBROD (Smooth Backbone-Reliant Orientation-Dependent) method uses only the backbone protein conformation, and hence it can be applied to scoring coarse-grained protein models. The proposed method deduces its scoring function from a training set of protein models. The SBROD scoring function is composed of four terms related to different structural features: residue–residue orientations, contacts between backbone atoms, hydrogen bonding and solvent–solute interactions. It is smooth with respect to atomic coordinates and thus is potentially applicable to continuous gradient-based optimization of protein conformations. Furthermore, it can also be used for coarse-grained protein modeling and computational protein design. SBROD proved to achieve similar performance to state-of-the-art single-model QA methods on diverse datasets (CASP11, CASP12 and MOULDER). Availability and implementation The standalone application implemented in C++ and Python is freely available at https://gitlab.inria.fr/grudinin/sbrod and supported on Linux, MacOS and Windows. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MetaMQAP: A meta-server for the quality assessment of protein models

2008 ◽  
Vol 9 (1) ◽  
Author(s):  
Marcin Pawlowski ◽  
Michal J Gajda ◽  
Ryszard Matlak ◽  
Janusz M Bujnicki
Keyword(s):  
Quality Assessment ◽  
Protein Models

scholarly journals Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

2013 ◽  
Vol 14 (5) ◽  
pp. 9893-9905 ◽  
Author(s):  
Jacek Wabik ◽  
Sebastian Kmiecik ◽  
Dominik Gront ◽  
Maksim Kouza ◽  
Andrzej Koliński
Keyword(s):  
Molecular Dynamics ◽  
Coarse Grained ◽  
Replica Exchange ◽  
Protein Models

scholarly journals Necessity of High Physical Resolution in the Development of Flexible Coarse-Grained Protein Models

2015 ◽  
Vol 108 (2) ◽  
pp. 161a
Author(s):  
ZhiGuang Jia ◽  
Jianhan Chen
Keyword(s):  
Coarse Grained ◽  
Protein Models

scholarly journals The ModFOLD4 server for the quality assessment of 3D protein models

2013 ◽  
Vol 41 (W1) ◽  
pp. W368-W372 ◽  
Author(s):  
Liam J. McGuffin ◽  
Maria T. Buenavista ◽  
Daniel B. Roche
Keyword(s):  
Quality Assessment ◽  
Protein Models

scholarly journals SELECTIVE ADVANTAGE OF RECOMBINATION IN EVOLVING PROTEIN POPULATIONS: A LATTICE MODEL STUDY

2006 ◽  
Vol 17 (01) ◽  
pp. 75-90 ◽  
Author(s):  
PAUL D. WILLIAMS ◽  
DAVID D. POLLOCK ◽  
RICHARD A. GOLDSTEIN
Keyword(s):  
Homologous Recombination ◽  
Lattice Model ◽  
Selective Advantage ◽  
Native Structure ◽  
Fitness Level ◽  
Model Study ◽  
Protein Model ◽  
Evolutionary Advantage ◽  
Protein Models ◽  
Mutational Processes

Recent research has attempted to clarify the contributions of several mutational processes, such as substitutions or homologous recombination. Simplistic, tractable protein models, which determine the compact native structure phenotype from the sequence genotype, are well-suited to such studies. In this paper, we use a lattice-protein model to examine the effects of point mutation and homologous recombination on evolving populations of proteins. We find that while the majority of mutation and recombination events are neutral or deleterious, recombination is far more likely to be beneficial. This results in a faster increase in fitness during evolution, although the final fitness level is not significantly changed. This transient advantage provides an evolutionary advantage to subpopulations that undergo recombination, allowing fixation of recombination to occur in the population.

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