ArticleJournal of computational chemistry2014
LEAP: highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains.
Article in Journal of computational chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Highly Accurate and Efficient Deep Learning Paradigm for Full-Atom Protein Loop Modeling with KarmaLoop.Research (Washington, D.C.) · 2024Article
- Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency.Briefings in bioinformatics · 2023Article
- Accurate positioning of functional residues with robotics-inspired computational protein design.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Article
- Transient local secondary structure in the intrinsically disordered C-term of the Albino3 insertase.Biophysical journal · 2021Article
- DaReUS-Loop: a web server to model multiple loops in homology models.Nucleic acids research · 2019Article
- Computational design of structured loops for new protein functions.Biological chemistry · 2019Review
- DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins.Scientific reports · 2018Article
- 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
- SL2: an interactive webtool for modeling of missing segments in proteins.Nucleic acids research · 2016Article
- LoopIng: a template-based tool for predicting the structure of protein loops.Bioinformatics (Oxford, England) · 2015Article
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Authors and funding
3 authors.
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Abstract
Prediction of protein loop conformations without any prior knowledge (ab initio prediction) is an unsolved problem. Its solution will significantly impact protein homology and template-based modeling as well as ab initio protein-structure prediction. Here, we developed a coarse-grained, optimized scoring function for initial sampling and ranking of loop decoys. The resulting decoys are then further optimized in backbone and side-chain conformations and ranked by all-atom energy scoring functions. The final integrated technique called loop prediction by energy-assisted protocol achieved a median value of 2.1 Å root mean square deviation (RMSD) for 325 12-residue test loops and 2.0 Å RMSD for 45 12-residue loops from critical assessment of structure-prediction techniques (CASP) 10 target proteins with native core structures (backbone and side chains). If all side-chain conformations in protein cores were predicted in the absence of the target loop, loop-prediction accuracy only reduces slightly (0.2 Å difference in RMSD for 12-residue loops in the CASP target proteins). The accuracy obtained is about 1 Å RMSD or more improvement over other methods we tested. The executable file for a Linux system is freely available for academic users at http://sparks-lab.org.
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