Journal Article10.1002/JCC.10349
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
Yong Duan,Chun Wu,Shibasish Chowdhury,Mathew C. Lee,Guoming Xiong,Wei Zhang,Rong Yang,Piotr Cieplak,Piotr Cieplak,Ray Luo,Tai-Sung Lee,Tai-Sung Lee,James W. Caldwell,Junmei Wang,Peter A. Kollman +14 more
TL;DR: A third‐generation point‐charge all‐atom force field for proteins is developed and initial tests on peptides demonstrated a high‐degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace‐Gly‐nme and Ace‐Ala‐Nme di‐peptides.
read more
Abstract: Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of e = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1999–2012, 2003
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Dynamic cooperation of hydrogen binding and π stacking in ssDNA adsorption on graphene oxide
TL;DR: This work shows that an ssDNA segment could be stably adsorbed on a GO surface through hydrogen bonding and π-π stacking interactions, with preferential binding to the oxidized rather than to the unoxidized region of the GO surface.
73
Choline Ion Interactions with DNA Atoms Explain Unique Stabilization of A–T Base Pairs in DNA Duplexes: A Microscopic View
TL;DR: The unique binding interactions of choline ions with DNA atoms are elucidated from a microscopic viewpoint using molecular dynamics simulations to provide new insight into the stability of DNA duplexes under crowding conditions found in living cells.
73
Taxifolin prevents postprandial hyperglycemia by regulating the activity of α‐amylase: Evidence from an in vivo and in silico studies
TL;DR: TFN might be a potent inhibitor of α‐amylase that has the potential to regulate the postprandial hyperglycemia along with its anti‐inflammatory and anti‐oxidant properties during the treatment of DM.
73
CG2AA: Backmapping Protein Coarse-Grained Structures
TL;DR: A computer program is presented that accurately reconstructs the atomistic structure from a CG model for proteins, using a simple geometrical algorithm, and this structure can be analyzed by itself or used as an onset for atomistic molecular dynamics simulations.
Model of glycoprotein hormone receptor ligand binding and signaling.
William R. Moyle,Yongna Xing,Win Lin,Donghui Cao,Rebecca V. Myers,John E. Kerrigan,Michael P. Bernard +6 more
TL;DR: The region that links the lutropin receptor leucine-rich repeat domain (LRD) to its transmembrane domain (TMD) has substantial roles in ligand binding and signaling, hence the signaling specificity domain (SSD).
73
References
Density‐functional thermochemistry. III. The role of exact exchange
TL;DR: In this article, a semi-empirical exchange correlation functional with local spin density, gradient, and exact exchange terms was proposed. But this functional performed significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
TL;DR: Numerical calculations on a number of atoms, positive ions, and molecules, of both open- and closed-shell type, show that density-functional formulas for the correlation energy and correlation potential give correlation energies within a few percent.
94.9K
Comparison of simple potential functions for simulating liquid water
TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
39.4K
A smooth particle mesh Ewald method
TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
21.3K
Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions
TL;DR: In this paper, a reliable procedure for calculating the electron affinity of an atom and present results for hydrogen, boron, carbon, oxygen, and fluorine (hydrogen is included for completeness).