ArticleThe journal of physical chemistry. B2011
Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed.
- A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.Journal of computational chemistry · 2018Article
- Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains.The journal of physical chemistry. B · 2017Article
- Theoretical Studies of Interactions between O-Phosphorylated and Standard Amino-Acid Side-Chain Models in Water.The journal of physical chemistry. B · 2015Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
- Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions.Journal of chemical theory and computation · 2015Article
- Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations.Journal of chemical theory and computation · 2015Article
- A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.Journal of molecular modeling · 2014Article
- The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.Chemical Society reviews · 2014Review
- Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field.Journal of chemical theory and computation · 2014Article
- Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.Journal of chemical theory and computation · 2013Article
- Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.Journal of chemical theory and computation · 2013Article
- Lessons from application of the UNRES force field to predictions of structures of CASP10 targets.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues.Journal of chemical theory and computation · 2012Article
- Toward temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. II. Molecular dynamics study of pairs of different types of interactions in water at various temperatures.The journal of physical chemistry. B · 2012Article
- A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the β amyloid peptide (Aβ(1-28)).The journal of physical chemistry. B · 2011Article
- Coarse-grained force field: general folding theory.Physical chemistry chemical physics : PCCP · 2011Review
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 two-site coarse-grained model for the interactions of charged side chains, to be used with our coarse-grained UNRES force field for protein simulations proposed in the accompanying paper, has been extended to pairs of oppositely charged side chains. The potentials of mean force of four pairs of molecules modeling charged amino-acid side chains, i.e., propionate-n-pentylamine cation (for aspartic acid-lysine), butyrate-n-pentylamine cation (for glutamic acid-lysine), propionate-1-butylguanidine (for aspartic acid-arginine), and butyrate-1-butylguanidine (for glutamic acid-arginine) pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expression was fitted to the potentials of mean force. Compared to pairs of like-charged side chains discussed in the accompanying paper, an average quadrupole-quadrupole interaction term had to be introduced to reproduce the Coulombic interactions, and a multistate model of charge distribution had to be introduced to fit the potentials of mean force of all oppositely charged pairs well. The model reproduces all salt-bridge minima and, consequently, is likely to improve the performance of the UNRES force field.
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.