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Mehr DetailsWater in the Active Site of Ketosteroid Isomerase
· Δ 5-3 Ketosteroid isomerase (KSI) is an extensively studied enzyme that serves as a useful model system for the study of the role of hydrogen bonding in enzyme catalysis.Two homologous bacterial forms of this enzyme from Pseudomonas putida (pKSI) and Commamonas testosteroni (tKSI) have been studied. (tKSI) have been studied.
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Mehr DetailsRNA force field with accuracy comparable to state-of-the-art …
· The simulated structural and thermodynamic properties of these systems exhibited substantially improved agreement with experimental data, to the point that the accuracy of this revised AMBER RNA force field can be considered comparable to that of …
Mehr DetailsComparison of Accuracy and Convergence Rate between Equilibrium and Nonequilibrium Alchemical Transformations for Calculation …
· a State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China b NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China c Department of Chemistry and Biochemistry, University of Oklahoma, Norman OK 73019, USA ...
Mehr DetailsNeurotransmitter Funneling Optimizes Glutamate Receptor Kinetics: Neuron
WT and mutant glutamate receptors were overexpressed in HEK293 cells using calcium phosphate transfection. The external solution contained: 150 mM NaCl, 0.1 mM MgCl 2, 0.1 mM CaCl 2, and 5 mM HEPES, titrated to pH 7.3 with NaOH, to which we added drugs as required. Drugs were obtained from Ascent Scientific and Sigma.
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Mehr DetailsTemperature artifacts in protein structures bias ligand-binding …
X-ray crystallography is the gold standard to resolve conformational ensembles that are significant for protein function, ligand discovery, and computational methods development. However, relevant conformational states may be missed at common cryogenic (cryo ...
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The Journal of Chemical Theory and Computation Journal Impact IF 2020-2021 is 5.011. More IF Analysis, Trend, Ranking & Prediction.
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Mehr DetailsMultibody correlations in the hydrophobic solvation of glycine …
· II. THEORY Decomposing free energies into components can be challenging, as path dependencies in energy definitions can lead to difficulties in interpreting the results. Our chosen decomposition of ΔG vdw into ΔG rep and ΔG att according to a WCA decomposition, 17,18 in contrast, is a well-defined decomposition with a strictly defined path.
Mehr DetailsHow well do force fields capture the strength of salt bridges in proteins? [PeerJ]
Steinbrecher T, Zhu C, Wang L, Abel R, Negron C, Pearlman D, Feyfant E, Duan J, Sherman W. 2017. Predicting the effect of amino acid single-point mutations on protein stability—large-scale validation of MD-based relative free energy calculations. Journal of :
Mehr DetailsGrid inhomogeneous solvation theory: Hydration structure and …
· 1 Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0736, USA 2 Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York 10468, USA ...
Mehr DetailsHow well do force fields capture the strength of salt bridges in …
the results are less accurate when the mutations involve a change in charge (Steinbrecher et al., 2017). In addition to the DER correction described above, several groups have examined and modified the charges in protein force fields in order to provide a more
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Hummer-N Theresa Kröninger GER 8 penalties 76.69 sec bay / 9y. / G / KWPN / Quasimodo Z / Ahorn Z / 106ES95 / Clementine & Theresa Kröninger 48. 619 Caligor Jacob Feyler GER 8 penalties 78.49 sec chest / 12y. / G / MECKL 49. 251
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Mehr DetailsInterlaced P3M algorithm with analytical and ik-differentiation…
· The interlacing technique of Hockney and Eastwood is extended to the particle-particle, particle-mesh (P3M) algorithm with analytical and ik-differentiation that computes the approximate Coulomb forces between N point particles in a periodic box. Interlacing means that one makes two separate computations of the reciprocal-space Ewald force, using two grids shifted with respect to …
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