ArticleProteins2008
Loop modeling: Sampling, filtering, and scoring.
Article in Proteins, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
72 citing papers in PubMed.
- Intermediate-state-trapped mutants pinpoint G protein-coupled receptor conformational allostery.Nature communications · 2023Article
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- Ten quick tips for homology modeling of high-resolution protein 3D structures.PLoS computational biology · 2020Article
- Simple Selection Procedure to Distinguish between Static and Flexible Loops.International journal of molecular sciences · 2020Article
- Extramembranous Regions in G Protein-Coupled Receptors: Cinderella in Receptor Biology?The Journal of membrane biology · 2019Review
- Conformational Dynamics of the HIV-Vif Protein Complex.Biophysical journal · 2019Article
- Mechanistic insights into allosteric regulation of the ANature communications · 2018Article
- Mechanism of Mechanosensitive Gating of the TREK-2 Potassium Channel.Biophysical journal · 2018Article
- The Tiam1 guanine nucleotide exchange factor is auto-inhibited by its pleckstrin homology coiled-coil extension domain.The Journal of biological chemistry · 2017Article
- Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.Bioinformatics (Oxford, England) · 2017Article
- Antibody H3 Structure Prediction.Computational and structural biotechnology journal · 2017Review
- RCD+: Fast loop modeling server.Nucleic acids research · 2016Article
- Non-degradative Ubiquitination of Protein Kinases.PLoS computational biology · 2016Article
- Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor?Biophysical journal · 2015Article
- Conformational sampling and structure prediction of multiple interacting loops in soluble and β-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method.Bioinformatics (Oxford, England) · 2015Article
- Approaching rational epitope vaccine design for hepatitis C virus with meta-server and multivalent scaffolding.Scientific reports · 2015Article
- Post-translational environmental switch of RadA activity by extein-intein interactions in protein splicing.Nucleic acids research · 2015Article
- Article
- Antibody modeling using the prediction of immunoglobulin structure (PIGS) web server [corrected].Nature protocols · 2014Article
12 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
We describe a fast and accurate protocol, LoopBuilder, for the prediction of loop conformations in proteins. The procedure includes extensive sampling of backbone conformations, side chain addition, the use of a statistical potential to select a subset of these conformations, and, finally, an energy minimization and ranking with an all-atom force field. We find that the Direct Tweak algorithm used in the previously developed LOOPY program is successful in generating an ensemble of conformations that on average are closer to the native conformation than those generated by other methods. An important feature of Direct Tweak is that it checks for interactions between the loop and the rest of the protein during the loop closure process. DFIRE is found to be a particularly effective statistical potential that can bias conformation space toward conformations that are close to the native structure. Its application as a filter prior to a full molecular mechanics energy minimization both improves prediction accuracy and offers a significant savings in computer time. Final scoring is based on the OPLS/SBG-NP force field implemented in the PLOP program. The approach is also shown to be quite successful in predicting loop conformations for cases where the native side chain conformations are assumed to be unknown, suggesting that it will prove effective in real homology modeling applications.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.