ArticleProteins2010
Improved side-chain torsion potentials for the Amber ff99SB protein force field.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2,566 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
2,566 citing papers in PubMed, 6,153 citations in OpenAlex.
- Analyses of receptor binding specificity of highly pathogenic avian influenza A (H5N1) viruses isolated from felines in South Korea, 2023.Virulence · 2026Article
- Structure-guided discovery of novel ERα-binding peptides with in vitro antiproliferative activity.Journal of enzyme inhibition and medicinal chemistry · 2026Article
- Structure-function insights into the digestive fate of angiotensin-converting enzyme-inhibitory peptides from microwave-treated corn gluten meal.Food chemistry. Molecular sciences · 2026Article
- Computational evaluation of EPA-PC binding to GCase in neuronopathic Gaucher disease.Current research in structural biology · 2026Article
- Potential molecular links between triclosan exposure and osteoarthritis: An integrative systems toxicology study.iScience · 2026Article
- From Closed to Mighty: How GTP-Induced Allosteric Dynamics, Dimerization, and Membrane Binding Transform a Bacterial Dynamin-like Protein.Journal of chemical information and modeling · 2026Article
- PI3Kδ is selectively inhibited by roginolisib by stabilizing the C-terminal helix kα12.Nature communications · 2026Article
- Structural basis of nucleotide-dependent conformational switching of a CBS-family protein on the archaeal 50S ribosome.Science China. Life sciences · 2026Article
- Computational identification of potential inhibitors for chikungunya virus nsP2pro.Royal Society open science · 2026Article
- Quasi-continuous cotranslational compaction and folding of a multidomain protein.Nature communications · 2026Article
- Optimization of enzymatic hydrolysis for generating potential multifunctional peptides from goat milk: Bioactivity evaluation, structural characterization and molecular interaction analysis.Food chemistry: X · 2026Article
- Pre-activation and gating pathway of AMPA receptors revealed by full and partial agonists.Nature structural & molecular biology · 2026Article
- Cancer treatment alters mutant selection in normal esophagus.Nature genetics · 2026Article
- Conformation- and Compound-Dependence of Ribose/2'-Deoxyribose Retention Patterns in Pyrimidine-Nucleoside Phosphorylase fromACS omega · 2026Article
- A Single Amino Acid in the A2 Linker of Cholera Toxin Affects the Efficiency of Toxin Disassembly and Resulting Toxicity.ACS omega · 2026Article
- Electronic-Structure Determinants of Flavonoid Inhibition at the Molybdenum Cofactor of Xanthine Oxidase: A QM/MM Study.ACS omega · 2026Article
- Integration of network pharmacology, structure-based pharmacophore modeling, DFT, molecular docking, and molecular dynamics simulations to identify multi-target small molecule inhibitors against Alzheimer's disease.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- In Vitro Antioxidant Activity and Dual-Target Inhibitory Effects of Dipyridamole on α-Amylase and α-Glucosidase: Molecular Mechanisms and Molecular Dynamics Simulations.Biomolecules · 2026Article
- Comparative Genomics-Guided Epitope Prioritization and in Silico Design of a Multi-Epitope DNA Vaccine Candidate Against Megalocytivirus pagrus 1.Marine biotechnology (New York, N.Y.) · 2026Article
- Engineering a genetic construct to express soluble proteins tethered to the cell membrane.Bioscience reports · 2026Article
2,506 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
7 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the Amber ff99SB force field. First, we used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, we optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mechanical calculations. Finally, we used microsecond-timescale MD simulations in explicit solvent to validate the resulting force field against a large set of experimental NMR measurements that directly probe side-chain conformations. The new force field, which we have termed Amber ff99SB-ILDN, exhibits considerably better agreement with the NMR data.
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.