Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine “dipeptides” (Ace‐Ala‐Nme and Ace‐Gly‐Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

Keywords

Force field (fiction), Molecular mechanics, Chemistry, Molecular dynamics, Intramolecular force

References

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Cited by

• QM/MM investigations of organic chemistry oriented questions.Thomas Schmidt, Alexander Paasche, Christoph Grebner — 2014
• Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes淑子 大久保, 至 叶内, 弘貴 大野 — 2009
• ORGANIZING FORCES AND CONFORMATIONAL ACCESSIBILITY IN THE UNFOLDED STATE OF PROTEINSNicholas C. Fitzkee — 2006
• Seamless Integration of URL-Addresable Sources: The Websheet ProjectM. J. Horgan, Óscar Díaz — 2002
• Innovations: the gas is greener.Lance Frazer — 2002
• Boundary value approaches to molecular dynamics simulationP. Vedell — 2007
• Towards a Unification of Supercomputing, Molecular Dynamics Simulation and Experimental Neutron and X-ray Scattering TechniquesBenjamin Lindner — 2012
• Force field comparison through computational analysis of capsular polysaccharides of Streptococcus pneumoniae serotypes 19A and FMarc Brian Gordon — 2014
• Hydrogen bonds in molecular mechanics force fields.Jan Hermans — 2005
• Statistical approaches to the study of protein folding and energeticsNikolas S. Burkoff — 2014
• Effect of pH on the Aggregation of α-syn12 Dimer in Explicit Water by Replica-Exchange Molecular Dynamics SimulationZanxia Cao, Xiumei Zhang, Lei Liu — 2015
• Promise of advances in simulation methods for protein crystallography: implicit solvent models, time-averaging refinement, and quantum mechanical modeling.Celia A. Schiffer, Jan Hermans — 2003
• Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamicsAbil E. Aliev, Martin Kulke, Harmeet S. Khaneja — 2014
• Exploring peptide energy landscapes: A test of force fields and implicit solvent modelsPeter Steinbach — 2004
• Comparisons of force fields for proteins by generalized-ensemble simulationsTakao Yoda, Yuji Sugita, Yuko Okamoto — 2004
• Kinetics of contact formation and end-to-end distance distributions of swollen disordered peptides.Andrea Soranno, Renato Longhi, Tommaso Bellini — 2009
• Effects of pH and Temperature on the Structural and Thermodynamic Character of a-syn12 Peptide in Aqueous SolutionZanxia Cao, Lei Liu, Jihua Wang — 2010
• The role of plastic beta-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein.Hongxing Lei, Yong Duan — 2004
• Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor InteractionsSiobhan Toal, Reinhard Schweitzer‐Stenner — 2014
• Molecular modeling of different substrate‐binding modes and their role in penicillin acylase catalysisFedor N. Novikov, Oleg V. Stroganov, Ilyas G. Khaliullin — 2013

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