ArticleBiophysical journal2015
Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- The prevalence of protein misfolding as a mechanism for hereditary deafness.PLoS genetics · 2026Article
- Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.The Journal of chemical physics · 2024Article
- A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model.The Journal of chemical physics · 2023Article
- Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.Journal of chemical theory and computation · 2021Article
- Syngeneic homograft of framework regions enhances the affinity of the mouse anti-human epidermal receptor 2 single-chain antibody e23sFv.Experimental and therapeutic medicine · 2021Article
- Novel IntragenicCurrent eye research · 2020Article
- Protein Design by Provable Algorithms.Communications of the ACM · 2019Article
- Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking.Biophysical journal · 2019Article
- Effective mismatch repair depends on timely control of PCNA retention on DNA by the Elg1 complex.Nucleic acids research · 2019Article
- Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods.Journal of molecular biology · 2018Article
- Tinker 8: Software Tools for Molecular Design.Journal of chemical theory and computation · 2018Article
- Computer-aided design of amino acid-based therapeutics: a review.Drug design, development and therapy · 2018Review
- LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- LADD syndrome with glaucoma is caused by a novel gene.Molecular vision · 2017Article
- Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.Physical chemistry chemical physics : PCCP · 2016Article
- Identification of New Mutations at the PCNA Subunit Interface that Block Translesion Synthesis.PloS one · 2016Article
- Long-Term Follow-Up on a Juvenile Open-Angle Glaucoma Pedigree with a Novel EFEMP1 Mutation (c.1313, p.Tyr438Cys).Ophthalmology. GlaucomaArticle
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Authors and funding
9 authors.
Funding
Abstract
A balance of van der Waals, electrostatic, and hydrophobic forces drive the folding and packing of protein side chains. Although such interactions between residues are often approximated as being pairwise additive, in reality, higher-order many-body contributions that depend on environment drive hydrophobic collapse and cooperative electrostatics. Beginning from dead-end elimination, we derive the first algorithm, to our knowledge, capable of deterministic global repacking of side chains compatible with many-body energy functions. The approach is applied to seven PCNA x-ray crystallographic data sets with resolutions 2.5-3.8 Å (mean 3.0 Å) using an open-source software. While PDB_REDO models average an Rfree value of 29.5% and MOLPROBITY score of 2.71 Å (77th percentile), dead-end elimination with the polarizable AMOEBA force field lowered Rfree by 2.8-26.7% and improved mean MOLPROBITY score to atomic resolution at 1.25 Å (100th percentile). For structural biology applications that depend on side-chain repacking, including x-ray refinement, homology modeling, and protein design, the accuracy limitations of pairwise additivity can now be eliminated via polarizable or quantum mechanical potentials.
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