ArticleJournal of molecular modeling2014
A consistent force field parameter set for zwitterionic amino acid residues.
Article in Journal of molecular modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed, 50 citations in OpenAlex.
- Restoring brain functions in the Mo-blo mouse model of Menkes disease with copper nanoclusters.Science advances · 2026Article
- Fibrosis suppressive effect and mechanism of CaSR positive allosteric modulators/p-dioxanone copolymers.Drug delivery and translational research · 2026Article
- Structural basis for pH-responsive amino acid transport via SLC7A4.Nature communications · 2026Article
- Chiral Ligand-Protected Gold Nanoclusters as Biosensors for Small Chiral Biomolecules: A Computational Study.ACS nano · 2026Article
- Transition State-Based Computational Enzyme Design.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Unveiling the Catalytic Mechanism and Conformational Dynamics of Guinea Pig l‑Asparaginase Type 1 for Leukemia Drug Design.ACS catalysis · 2025Article
- Why Is Arginine the Only Amino Acid That Inhibits Polyglutamine Monomers from Taking on Toxic Conformations?ACS chemical neuroscience · 2024Article
- Elucidation of the Active Form and Reaction Mechanism in Human Asparaginase Type III Using Multiscale Simulations.Journal of chemical information and modeling · 2023Article
- Electrostatic Ratchet for Successive Peptide Synthesis in Nonribosomal Molecular Machine RimK.Journal of the American Chemical Society · 2023Article
- Binary and Ternary Complexes of Cucurbit[8]uril with Tryptophan, Phenylalanine, and Tyrosine: A Computational Study.ACS omega · 2022Article
- Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation.PLoS computational biology · 2022Article
- An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid.Chemical science · 2021Article
- State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane.PLoS computational biology · 2021Article
- Conserved Dynamic Mechanism of Allosteric Response to L-arg in Divergent Bacterial Arginine Repressors.Molecules (Basel, Switzerland) · 2020Article
- A Refined Open State of the Glycine Receptor Obtained via Molecular Dynamics Simulations.Structure (London, England : 1993) · 2020Article
- Proton Control of Transitions in an Amino Acid Transporter.Biophysical journal · 2019Article
- Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA Receptors.Biophysical journal · 2018Article
- Hydration of the Carboxylate Group in Anti-Inflammatory Drugs: ATR-IR and Computational Studies of Aqueous Solution of Sodium Diclofenac.ACS omega · 2018Article
- Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.Journal of chemical theory and computation · 2017Article
- Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization.The journal of physical chemistry. B · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Isolated amino acids play an important role in biochemistry and are therefore an interesting object of study. Atomistic molecular dynamics (MD) simulations can provide a high-resolution picture of the dynamic features of these species, especially in their biological environment. Unfortunately, most standard force field packages lack libraries for isolated amino acids in their zwitterionic form. Although several studies have used ad-hoc parameterizations for single amino acids, a consistent force-field parameter set for these molecules is still missing. Here, we present such a parameter library derived from the widely used parm99SB set from the AMBER program package. The parameter derivation for all 20 proteinogenic amino acids transparently followed established procedures with histidine treated in three different protonation states. All amino acids were subjected to MD simulations in four different forms for comparison: zwitterionic, N-teminally capped with acetyl, C-terminally capped with N-methyl, and capped at both termini. Simulation results show similarities between the different forms. Five zwitterionic amino acids-arginine, glutamate, glycine, phenylalanine, leucine-were simulated in a protein environment. Proteins and ligands generally retained their initial structure. The new parameter set will thus facilitate future atomistic simulations of these species.
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.