ArticleProteins2016
FF12MC: A revised AMBER forcefield and new protein simulation protocol.
Article in Proteins, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 42 citations in OpenAlex.
- Article
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- Design of synthetic collagens that assemble into supramolecular banded fibers as a functional biomaterial testbed.Nature communications · 2022Article
- Computational design of a sensitive, selective phase-changing sensor protein for the VX nerve agent.Science advances · 2022Article
- Discovery of a Natural Product with Potent Efficacy Against SARS-CoV-2 by Drug Screening.Interdisciplinary sciences, computational life sciences · 2022Article
- How neocarcerand Octacid4 self-assembles with guests into irreversible noncovalent complexes and what accelerates the assembly.Communications chemistry · 2022Article
- TREM2 interacts with TDP-43 and mediates microglial neuroprotection against TDP-43-related neurodegeneration.Nature neuroscience · 2022Article
- HD5 and LL-37 Inhibit SARS-CoV and SARS-CoV-2 Binding to Human ACE2 by Molecular Simulation.Interdisciplinary sciences, computational life sciences · 2021Article
- Enzymatic activation of pyruvate kinase increases cytosolic oxaloacetate to inhibit the Warburg effect.Nature metabolism · 2021Article
- How the water-soluble hemicarcerand incarcerates guests at room temperature decoded with modular simulations.Communications chemistry · 2021Article
- CFAP45 deficiency causes situs abnormalities and asthenospermia by disrupting an axonemal adenine nucleotide homeostasis module.Nature communications · 2020Article
- Characterization of an alternative BAK-binding site for BH3 peptides.Nature communications · 2020Article
- Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications.International journal of molecular sciences · 2019Review
- Why Computed Protein Folding Landscapes Are Sensitive to the Water Model.Journal of chemical theory and computation · 2019Article
- Remote Activation of a Latent Epitope in an Autoantigen Decoded With Simulated B-Factors.Frontiers in immunology · 2019Article
- Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15.The journal of physical chemistry. B · 2017Article
- Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Specialized to simulate proteins in molecular dynamics (MD) simulations with explicit solvation, FF12MC is a combination of a new protein simulation protocol employing uniformly reduced atomic masses by tenfold and a revised AMBER forcefield FF99 with (i) shortened CH bonds, (ii) removal of torsions involving a nonperipheral sp(3) atom, and (iii) reduced 1-4 interaction scaling factors of torsions ϕ and ψ. This article reports that in multiple, distinct, independent, unrestricted, unbiased, isobaric-isothermal, and classical MD simulations FF12MC can (i) simulate the experimentally observed flipping between left- and right-handed configurations for C14-C38 of BPTI in solution, (ii) autonomously fold chignolin, CLN025, and Trp-cage with folding times that agree with the experimental values, (iii) simulate subsequent unfolding and refolding of these miniproteins, and (iv) achieve a robust Z score of 1.33 for refining protein models TMR01, TMR04, and TMR07. By comparison, the latest general-purpose AMBER forcefield FF14SB locks the C14-C38 bond to the right-handed configuration in solution under the same protein simulation conditions. Statistical survival analysis shows that FF12MC folds chignolin and CLN025 in isobaric-isothermal MD simulations 2-4 times faster than FF14SB under the same protein simulation conditions. These results suggest that FF12MC may be used for protein simulations to study kinetics and thermodynamics of miniprotein folding as well as protein structure and dynamics. Proteins 2016; 84:1490-1516. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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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.