ArticleJournal of chemical theory and computation2015
Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field.
Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 316 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
316 citing papers in PubMed.
- From GROMACS Molecular Dynamics Simulations to Electronic Absorption Spectra: A Tutorial for Small Molecules in Organic Solvents.Journal of chemical education · 2026Article
- Rational design of triazole tyrosinase inhibitors via integrated free energy calculations.Molecular diversity · 2026Article
- Antibody-drug conjugate engineering: from design to efficacy and safety.Signal transduction and targeted therapy · 2026Review
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- Discovery of a cryptic aminoacidic triad involved in the temperature adaptation of GH1 enzymes.The FEBS journal · 2026Article
- Machine Learning-Driven Discovery of Indole/Oxoindole-Piperazine Scaffolds as Dual MAO-B/Sig-1R Ligands for Neurodegenerative Disorders.Journal of chemical information and modeling · 2026Article
- The Effect of CuACS chemical neuroscience · 2026Article
- Molecular modelling of the adipokinetic hormone receptor from the stick insect Carausius morosus, and its endogenous agonist.Scientific reports · 2026Article
- Nearest-Neighbor Effects in Short Unfolded Peptides: An Assessment of Molecular Dynamics Force Fields.Journal of chemical information and modeling · 2026Article
- Fast Fourier Transform Enables Automated Parametrization of Complex Dihedral Potentials in All-Atom and Coarse-Grained Force Fields.Journal of chemical information and modeling · 2026Article
- Structural basis for uracil removal from DNA by human SMUG1.Nature communications · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Targeting Middle East Respiratory Syndrome Coronavirus Spike Fusion Machinery With Antiviral Peptides: In Silico Exploration of the Heptad Repeat 2 Domain.MicrobiologyOpen · 2026Article
- Structural Modulation and Binding of HLA-DQ8 by Cysteine-to-Serine Mutated Insulin Peptide: Insights from Molecular Dynamics Simulations.International journal of molecular sciences · 2026Article
- Thermodynamic Activation Parameters for Chemical Reactions in Enzymes and Solution from Computer Simulations at a Single Temperature.Journal of chemical theory and computation · 2026Article
- Multi-scale computational insights into West Nile virus E-protein adsorption on graphene and phosphorene nanomaterials.Nanoscale advances · 2026Article
- Thermoresponsive Polymers under Solvent Flow through Molecular Dynamics.The journal of physical chemistry. B · 2026Article
- Mapping Still Matters: Coarse-Graining with Machine Learning Potentials.Journal of chemical information and modeling · 2026Article
- CH•••S hydrogen bonds drive molecular recognition of ergothioneine by the microbial transporter.Science advances · 2026Article
- Latent thermodynamic flows: unified representation learning and generative modeling of temperature-dependent behaviors from limited data.Chemical science · 2026Article
256 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1, and χ2 potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields.
Indexed as
Identifiers
What OpenQuestion holds
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.