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William Swope · SciRah

Researcher profile · Semantic Scholar

William Swope

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William Swope — researcher profile on SciRah

ORCID iD 0000-0002-5299-4145

h-index: 28
Works: 65
Citations: 7,310

Most-cited papers

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.
Hans W. Horn, William Swope, J. Pitera, J. Madura +3 more
2004Journal of Chemical Physics2,003 citations
Semantic Scholar
Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
M. Shirts, J. Pitera, William Swope, V. Pande
2003612 citations Open access
Semantic Scholar
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.
J. Chodera, N. Singhal, V. Pande, K. Dill +1 more
2007Journal of Chemical Physics606 citations
Semantic Scholar
Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations.
J. Chodera, William Swope, J. Pitera, Chaok Seok +1 more
2007Journal of Chemical Theory and Computation454 citations Open access
Semantic Scholar
Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory
William Swope, J. Pitera, F. Suits
2004448 citations
Semantic Scholar
Understanding folding and design: Replica-exchange simulations of ``Trp-cage'' miniproteins
J. Pitera, William Swope
2003Proceedings of the National Academy of Sciences of the United States of America332 citations Open access
Semantic Scholar
DiscoveryLink: A system for integrated access to life sciences data sources
L. Haas, P. Schwarz, P. Kodali, Elon Kotlar +2 more
2001IBM Systems Journal305 citations
Semantic Scholar
Blue Gene: A vision for protein science using a petaflop supercomputer
F. Allen, G. Almási, W. Andreoni, D. Beece +48 more
2001IBM Systems Journal280 citations
Semantic Scholar
The reaction mechanism for the organocatalytic ring-opening polymerization of l-lactide using a guanidine-based catalyst: hydrogen-bonded or covalently bound?
A. Chuma, Hans W. Horn, William Swope, R. Pratt +6 more
2008Journal of the American Chemical Society236 citations
Semantic Scholar
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15
Lee-Ping Wang, K. McKiernan, Joseph Gomes, K. Beauchamp +5 more
2017Journal of Physical Chemistry B211 citations Open access
Semantic Scholar
Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations
J. Chodera, William Swope, J. Pitera, K. Dill
2006Multiscale Modeling & simulation206 citations Open access
Semantic Scholar
Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a β-Hairpin Peptide†
William Swope, J. Pitera, F. Suits, Michael Pitman +7 more
2004164 citations
Semantic Scholar
Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment.
Wei-Yuan Yang, J. Pitera, William Swope, M. Gruebele
2004Journal of Molecular Biology149 citations
Semantic Scholar
Characterization of the TIP4P-Ew water model: vapor pressure and boiling point.
Hans W. Horn, William Swope, J. Pitera
2005Journal of Chemical Physics121 citations
Semantic Scholar
Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization
D. Cerutti, J. Rice, William Swope, D. Case
2013Journal of Physical Chemistry B119 citations Open access
Semantic Scholar
ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
D. Cerutti, William Swope, J. Rice, D. Case
2014Journal of Chemical Theory and Computation102 citations Open access
Semantic Scholar
Alchemical prediction of hydration free energies for SAMPL
D. Mobley, Shaui Liu, D. Cerutti, William Swope +1 more
2011Journal of Computer-Aided Molecular Design84 citations Open access
Semantic Scholar
Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures.
J. Chodera, William Swope, Frank Noé, Jan-Hendrik Prinz +2 more
2011Journal of Chemical Physics67 citations Open access
Semantic Scholar
Toward a Standard Protocol for Micelle Simulation.
M. Johnston, William Swope, K. Jordan, P. Warren +3 more
2016Journal of Physical Chemistry B60 citations Open access
Semantic Scholar
Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L
B. Fitch, A. Rayshubskiy, M. Eleftheriou, T. Ward +10 more
2006International Conference on Conceptual Structures60 citations
Semantic Scholar
Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.
Jan-Hendrik Prinz, J. Chodera, V. Pande, William Swope +2 more
2011Journal of Chemical Physics52 citations Open access
Semantic Scholar
Accounting for polarization cost when using fixed charge force fields. I. Method for computing energy.
William Swope, Hans W. Horn, J. Rice
2010Journal of Physical Chemistry B50 citations
Semantic Scholar
Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide.
J. Pitera, I. Haque, William Swope
2006Journal of Chemical Physics44 citations
Semantic Scholar
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.
William Swope, Hans W. Horn, J. Rice
2010Journal of Physical Chemistry B36 citations
Semantic Scholar
Integrating life sciences data-with a little Garlic
L. Haas, P. Kodali, J. Rice, P. Schwarz +1 more
2000Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering36 citations
Semantic Scholar
Toward biodegradable nanogel star polymers via organocatalytic ROP.
E. Appel, V. Lee, Timothy T. Nguyen, M. McNeil +6 more
2012Chemical Communications34 citations
Semantic Scholar
Comparison of computational approaches for predicting the effects of missense mutations on p53 function.
L. Chong, J. Pitera, William Swope, V. Pande
2009Journal of Molecular Graphics and Modelling34 citations
Semantic Scholar
Observation of noncooperative folding thermodynamics in simulations of 1BBL.
J. Pitera, William Swope, F. F. Abraham
2008Biophysical Journal30 citations Open access
Semantic Scholar
Challenge to Reconcile Experimental Micellar Properties of the CnEm Nonionic Surfactant Family.
William Swope, M. Johnston, A. Duff, J. McDonagh +4 more
2019Journal of Physical Chemistry B27 citations
Semantic Scholar
Collaborative assessment of molecular geometries and energies from the Open Force Field
Lorenzo D’Amore, D. F. Hahn, David L. Dotson, Joshua T. Horton +15 more
2022Journal of Chemical Information and Modeling26 citations Open access
Semantic Scholar
QM/MM-Based Fitting of Atomic Polarizabilities for Use in Condensed-Phase Biomolecular Simulation.
C. Vosmeer, Ariën S. Rustenburg, J. Rice, Hans W. Horn +2 more
2012Journal of Chemical Theory and Computation20 citations
Semantic Scholar
Correlation of early orientational ordering of engineered λ6–85 structure with kinetics and thermodynamics
E. Larios, J. Pitera, William Swope, M. Gruebele
200620 citations
Semantic Scholar
Blue Matter: Scaling of N-body simulations to one atom per node
B. Fitch, A. Rayshubskiy, M. Eleftheriou, T. Ward +5 more
2008IBM Journal of Research and Development19 citations
Semantic Scholar
Molecular Dynamics Simulations of Star Polymeric Molecules with Diblock Arms, a Comparative Study.
William Swope, Amber C. Carr, A. Parker, J. Sly +2 more
2012Journal of Chemical Theory and Computation18 citations
Semantic Scholar
Kinetic computational alanine scanning: application to p53 oligomerization.
L. Chong, William Swope, J. Pitera, V. Pande
2006Journal of Molecular Biology18 citations
Semantic Scholar
FLASHFLOOD: A 3D Field-based similarity search and alignment method for flexible molecules
Michael Pitman, W. Huber, Hans W. Horn, A. Krämer +2 more
2001J. Comput. Aided Mol. Des.17 citations
Semantic Scholar
The Effect of Different Occupational Background Noises on Voice Recognition Accuracy
Song Li, M. Yerebakan, Yue Luo, Ben A. Amaba +2 more
2022Journal of Computing and Information Science in Engineering16 citations
Semantic Scholar
Reducing lambda repressor to the core.
Maxim B. Prigozhin, Krishnarjun Sarkar, Dennis Law, William Swope +2 more
2011Journal of Physical Chemistry B16 citations
Semantic Scholar
Interfacial fluctuations of block copolymers: a coarse-grain molecular dynamics simulation study.
G. Srinivas, William Swope, J. Pitera
2007Journal of Physical Chemistry B16 citations
Semantic Scholar
A model for the simulation of the CnEm nonionic surfactant family derived from recent experimental results.
M. Johnston, A. Duff, Richard L. Anderson, William Swope
2020Journal of Physical Chemistry B15 citations Open access
Semantic Scholar
What can digitisation do for formulated product innovation and development?
J. McDonagh, William Swope, Richard L. Anderson, M. Johnston +1 more
202014 citations Open access
Semantic Scholar
The Role of Chemical Heterogeneity in Surfactant Adsorption at Solid-Liquid Interfaces.
J. Klebes, Sophie Finnigan, D. J. Bray, Richard L. Anderson +3 more
2020Journal of Chemical Theory and Computation14 citations Open access
Semantic Scholar
Overview of molecular dynamics techniques and early scientific results from the Blue Gene project
F. Suits, Michael Pitman, J. Pitera, William Swope +1 more
2005IBM Journal of Research and Development14 citations
Semantic Scholar
Deep computing for the life sciences
William Swope
2001IBM Systems Journal13 citations
Semantic Scholar
Influence of Solvent on the Drug-Loading Process of Amphiphilic Nanogel Star Polymers.
Amber C. Carr, V. Piunova, Hasmerya Maarof, J. Rice +1 more
2018Journal of Physical Chemistry B12 citations
Semantic Scholar
Custom math functions for molecular dynamics
R. Enenkel, B. Fitch, R. Germain, F. Gustavson +8 more
2005IBM Journal of Research and Development11 citations
Semantic Scholar
Large-scale collaborative assessment of binding free energy calculations for drug discovery using OpenFE
Hannah M. Baumann, Joshua T. Horton, Michael M. Henry, Alyssa Travitz +38 more
2026Journal of Chemical Information and Modeling9 citations Open access
Semantic Scholar
A QM/MM Derived Polarizable Water Model for Molecular Simulation
K. Visscher, William Swope, D. Geerke
2018Molecules9 citations Open access
Semantic Scholar
Role of hydrophilicity and length of diblock arms for determining star polymer physical properties.
Lisa E. Felberg, David H. Brookes, T. Head-Gordon, J. Rice +1 more
2015Journal of Physical Chemistry B9 citations Open access
Semantic Scholar
A robust approach to estimating rates from time-correlation functions
J. Chodera, Phillip J. Elms, William Swope, Jan-Hendrik Prinz +4 more
20119 citations
Semantic Scholar

Frequent co-authors

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J. Pitera×21
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J. Pitera — researcher profile on SciRah
J. Rice×14
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J. Rice — researcher profile on SciRah
V. Pande×8
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V. Pande — researcher profile on SciRah
Hans W. Horn×7
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Hans W. Horn — researcher profile on SciRah

×7

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Michael Pitman — researcher profile on SciRah

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J. Chodera — researcher profile on SciRah

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F. Suits — researcher profile on SciRah

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R. Germain — researcher profile on SciRah

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B. Fitch — researcher profile on SciRah

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T. Ward — researcher profile on SciRah

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M. Johnston — researcher profile on SciRah

Richard L. Anderson×5

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Richard L. Anderson — researcher profile on SciRah