ArticleProceedings of the National Academy of Sciences of the United States of America2009
Restriction versus guidance in protein structure prediction.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Artificial intelligence-based multi-objective optimization protocol for protein structure refinement.Bioinformatics (Oxford, England) · 2020Article
- Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins.The journal of physical chemistry. B · 2017Article
- UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling.Bioinformatics (Oxford, England) · 2016Article
- PEST Control of Molecular Stripping of NFκB from DNA Transcription Sites.The journal of physical chemistry. B · 2016Article
- Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.The journal of physical chemistry. B · 2016Article
- Toward a detailed understanding of search trajectories in fragment assembly approaches to protein structure prediction.Proteins · 2016Article
- Binding of NFκB Appears to Twist the Ankyrin Repeat Domain of IκBα.Biophysical journal · 2016Article
- De novo protein conformational sampling using a probabilistic graphical model.Scientific reports · 2015Article
- Residue-level global and local ensemble-ensemble comparisons of protein domains.Protein science : a publication of the Protein Society · 2015Article
- Learning To Fold Proteins Using Energy Landscape Theory.Israel journal of chemistry · 2014Article
- Investigation of the flexibility of protein kinases implicated in the pathology of Alzheimer's disease.Molecules (Basel, Switzerland) · 2014Article
- Structure of N-terminal sequence Asp-Ala-Glu-Phe-Arg-His-Asp-Ser of Aβ-peptide with phospholipase A2 from venom of Andaman Cobra sub-species Naja naja sagittifera at 2.0 Å resolution.International journal of molecular sciences · 2014Article
- Rapid sampling of local minima in protein energy surface and effective reduction through a multi-objective filter.Proteome science · 2013Article
- Detecting repetitions and periodicities in proteins by tiling the structural space.The journal of physical chemistry. B · 2013Article
- Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.BMC structural biology · 2013Article
- A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction.BMC structural biology · 2013Article
- AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing.The journal of physical chemistry. B · 2012Article
- Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface.Proteome science · 2012Article
- Article
- Rapid sampling of all-atom peptides using a library-based polymer-growth approach.Journal of computational chemistry · 2011Article
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5 authors.
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Abstract
Conformational restriction by fragment assembly and guidance in molecular dynamics are alternate conformational search strategies in protein structure prediction. We examine both approaches using a version of the associative memory Hamiltonian that incorporates the influence of water-mediated interactions (AMW). For short proteins (<70 residues), fragment assembly, while searching a restricted space, compares well to molecular dynamics and is often sufficient to fold such proteins to near-native conformations (4A) via simulated annealing. Longer proteins encounter kinetic sampling limitations in fragment assembly not seen in molecular dynamics which generally samples more native-like conformations. We also present a fragment enriched version of the standard AMW energy function, AMW-FME, which incorporates the local sequence alignment derived fragment libraries from fragment assembly directly into the energy function. This energy function, in which fragment information acts as a guide not a restriction, is found by molecular dynamics to improve on both previous approaches.
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