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William Swope

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Physiology

Protein Folding

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Publications

TOP 3
David S Cerutti; Julia E Rice; William C Swope; David A Case
Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization.
Eric A Appel; James L Hedrick; Victor Y Lee; Melanie McNeil; Robert D Miller; Fredrik Nederberg; Timothy T Nguyen; Jullia E Rice; William C Swope; Joseph Sly
Toward biodegradable nanogel star polymers via organocatalytic ROP.
David L Mobley; David S Cerutti; Shaui Liu; William C Swope; Julia E Rice
Alchemical prediction of hydration free energies for SAMPL.

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All Publications

2013: David S Cerutti; Julia E Rice; William C Swope; David A Case
Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization.
The journal of physical chemistry. B 2013;117(8):2328-38.
2012: Eric A Appel; James L Hedrick; Victor Y Lee; Melanie McNeil; Robert D Miller; Fredrik Nederberg; Timothy T Nguyen; Jullia E Rice; William C Swope; Joseph Sly
Toward biodegradable nanogel star polymers via organocatalytic ROP.
Chemical communications (Cambridge, England) 2012;48(49):6163-5.
2012: David L Mobley; David S Cerutti; Shaui Liu; William C Swope; Julia E Rice
Alchemical prediction of hydration free energies for SAMPL.
Journal of computer-aided molecular design 2012;26(5):551-62.
2011: Jan-Hendrik Prinz; Jeremy C Smith; William C Swope; John D Chodera; Vijay S Pande; Frank Noé
Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.
The Journal of chemical physics 2011;134(24):244108.
2011: John D Chodera; Frank Noé; Jan-Hendrik Prinz; Michael R Shirts; William C Swope; Vijay S Pande
Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures.
The Journal of chemical physics 2011;134(24):244107.
2010: William C Swope; Hans W Horn; Julia E Rice
Accounting for polarization cost when using fixed charge force fields. I. Method for computing energy.
The journal of physical chemistry. B 2010;114(26):8621-30.
2010: William C Swope; Hans W Horn; Julia E Rice
Accounting for polarization cost when using fixed charge force fields. II. Method and application for computing effect of polarization cost on free energy of hydration.
The journal of physical chemistry. B 2010;114(26):8631-45.
2008: Jed W Pitera; William C Swope; Farid F Abraham
Observation of noncooperative folding thermodynamics in simulations of 1BBL.
Biophysical journal 2008;94(12):4837-46.
2008: Anthony Chuma; Hans W Horn; William C Swope; Russell C Pratt; Lei Zhang; Bas G G Lohmeijer; Charles G Wade; Robert M Waymouth; James L Hedrick; Julia E Rice
The reaction mechanism for the organocatalytic ring-opening polymerization of l-lactide using a guanidine-based catalyst: hydrogen-bonded or covalently bound?
Journal of the American Chemical Society 2008;130(21):6749-54.
2007: Goundla Srinivas; William C Swope; Jed W Pitera
Interfacial fluctuations of block copolymers: a coarse-grain molecular dynamics simulation study.
The journal of physical chemistry. B 2007;111(49):13734-42.
2007: John D Chodera; Nina Singhal; Vijay S Pande; Ken A Dill; William C Swope
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.
The Journal of chemical physics 2007;126(15):155101.
2006: Jed W Pitera; Imran Haque; William C Swope
Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide.
The Journal of chemical physics 2006;124(14):141102.
2006: Lillian T Chong; William C Swope; Jed W Pitera; Vijay S Pande
Kinetic computational alanine scanning: application to p53 oligomerization.
Journal of molecular biology 2006;357(3):1039-49.
2005: Hans W Horn; William C Swope; Jed W Pitera
Characterization of the TIP4P-Ew water model: vapor pressure and boiling point.
The Journal of chemical physics 2005;123(19):194504.
2004: Hans W Horn; William C Swope; Jed W Pitera; Jeffry D Madura; Thomas J Dick; Greg L Hura; Teresa Head-Gordon
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.
The Journal of chemical physics 2004;120(20):9665-78.
2004: Wei Yuan Yang; Jed W Pitera; William C Swope; Martin Gruebele
Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment.
Journal of molecular biology 2004;336(1):241-51.
2003: Jed W Pitera; William C Swope
Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(13):7587-92.