William Swope

发表

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.

K. Dill, V. Pande, J. Chodera, 2007, The Journal of chemical physics.

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, 2004 .

Blue Gene: A vision for protein science using a petaflop supercomputer

Ajay K. Royyuru, José E. Moreira, Alessandro Curioni, 2001, IBM Syst. J..

Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment.

M. Gruebele, William Swope, J. Pitera, 2004, Journal of molecular biology.

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.

Greg L. Hura, Hans W. Horn, J. Madura, 2004, The Journal of chemical physics.

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15.

Joseph Gomes, Vijay S Pande, Kyle A Beauchamp, 2017, The journal of physical chemistry. B.

Toward a Standard Protocol for Micelle Simulation.

Richard L. Anderson, K. E. Jordan, Michael A. Johnston, 2016, The journal of physical chemistry. B.

Understanding folding and design: Replica-exchange simulations of ``Trp-cage'' miniproteins

William Swope, J. Pitera, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization.

D. Case, D. Cerutti, William Swope, 2013, The journal of physical chemistry. B.

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

D. Case, D. Cerutti, William Swope, 2014, Journal of chemical theory and computation.

Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory

William Swope, J. Pitera, F. Suits, 2004 .

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

Michael R. Shirts, M. Shirts, V. Pande, 2003 .

A QM/MM Derived Polarizable Water Model for Molecular Simulation

William Swope, D. Geerke, K. Visscher, 2018, Molecules.

Simulation and Experiments To Identify Factors Allowing Synthetic Control of Structural Features of Polymeric Nanoparticles.

William Swope, Robert D. Miller, J. Rice, 2016, The journal of physical chemistry. B.

An Efficient Algorithm for Topological Characterisation of Worm-Like and Branched Micelle Structures from Simulations.

Kirk P. Gardner, Richard L. Anderson, K. E. Jordan, 2020, Journal of chemical theory and computation.

QM/MM-Based Fitting of Atomic Polarizabilities for Use in Condensed-Phase Biomolecular Simulation.

Hans W. Horn, William C Swope, Ariën S Rustenburg, 2012, Journal of chemical theory and computation.

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.

Hans W. Horn, William C Swope, Hans W Horn, 2010, The journal of physical chemistry. B.

What Can Digitization Do For Formulated Product Innovation and Development

Richard L. Anderson, Michael A. Johnston, William Swope, 2020 .

Effect of Hydrophobic Core Topology and Composition on the Structure and Kinetics of Star Polymers: A Molecular Dynamics Study.

Lisa E. Felberg, William Swope, T. Head-Gordon, 2017, The journal of physical chemistry. B.

Interfacial fluctuations of block copolymers: a coarse-grain molecular dynamics simulation study.

William Swope, J. Pitera, G. Srinivas, 2007, The journal of physical chemistry. B.

Structural transition of nanogel star polymers with pH by controlling PEGMA interactions with acid or base copolymers

Greg L. Hura, Lisa E. Felberg, William Swope, 2016 .

The reaction mechanism for the organocatalytic ring-opening polymerization of l-lactide using a guanidine-based catalyst: hydrogen-bonded or covalently bound?

Hans W. Horn, J. Hedrick, William Swope, 2008, Journal of the American Chemical Society.

A model for the simulation of the CnEm nonionic surfactant family derived from recent experimental results.

Richard L. Anderson, Michael A. Johnston, William Swope, 2020, The journal of physical chemistry. B.

Chapter 6 Blue Matter: Scaling of N-Body Simulations to One Atom per Node

Robert S. Germain, Blake G. Fitch, Aleksandr Rayshubskiy, 2008 .

Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field

David L. Dotson, S. K. Lakkaraju, Joshua T. Horton, 2022, J. Chem. Inf. Model..

Water soluble, biodegradable amphiphilic polymeric nanoparticles and the molecular environment of hydrophobic encapsulates: Consistency between simulation and experiment

Julia E. Rice, William C. Swope, Victoria A. Piunova, 2015 .

Molecular Dynamics Simulations of Star Polymeric Molecules with Diblock Arms, a Comparative Study.

William Swope, Robert D. Miller, J. Rice, 2012, Journal of chemical theory and computation.

The Role of Chemical Heterogeneity in Surfactant Adsorption at Solid-Liquid Interfaces.

Richard L. Anderson, Michael A. Johnston, William Swope, 2020, Journal of chemical theory and computation.

Challenge to Reconcile Experimental Micellar Properties of the CnEm Nonionic Surfactant Family.

Richard L. Anderson, William C Swope, Michael A Johnston, 2019, The journal of physical chemistry. B.

Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide.

William C Swope, Jed W Pitera, William Swope, 2006, The Journal of chemical physics.

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations.

Ken A Dill, John D Chodera, William C Swope, 2007, Journal of chemical theory and computation.

Preface

Barry Robson, William C. Swope, James M. Coffin, 2001, IBM J. Res. Dev..

Blue Matter: Scaling of N-body simulations to one atom per node

Robert S. Germain, Mark Giampapa, Blake G. Fitch, 2008, IBM J. Res. Dev..

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.

Frank Noé, Vijay S Pande, Jan-Hendrik Prinz, 2011, The Journal of chemical physics.

Spatial Distribution of Hydrophobic Drugs in Model Nanogel-Core Star Polymers.

William Swope, Robert D. Miller, V. Prabhu, 2017, Macromolecules.

Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations

John D. Chodera, Ken A. Dill, Jed W. Pitera, 2006, Multiscale Model. Simul..

Observation of noncooperative folding thermodynamics in simulations of 1BBL.

William Swope, J. Pitera, F. Abraham, 2008, Biophysical journal.

The effect of workstation technology on methods in drug design and discovery

William C. Swope, David C. Spellmeyer, William Swope, 1993 .

Characterization of the TIP4P-Ew water model: vapor pressure and boiling point.

Hans W. Horn, William C Swope, Jed W Pitera, 2005, The Journal of chemical physics.

Deep computing for the life sciences

William C. Swope, William Swope, 2001, IBM Syst. J..

Kinetic computational alanine scanning: application to p53 oligomerization.

Vijay S Pande, William C Swope, Jed W Pitera, 2006, Journal of molecular biology.

Comparison of computational approaches for predicting the effects of missense mutations on p53 function.

Vijay S Pande, William C Swope, Jed W Pitera, 2009, Journal of molecular graphics & modelling.

Influence of Solvent on the Drug-Loading Process of Amphiphilic Nanogel Star Polymers.

William Swope, J. Rice, V. Piunova, 2018, The journal of physical chemistry. B.

A robust approach to estimating rates from time-correlation functions

Vijay S. Pande, John D. Chodera, William C. Swope, 2011, 1108.2304.

Role of hydrophilicity and length of diblock arms for determining star polymer physical properties.

David H. Brookes, Lisa E. Felberg, William Swope, 2015, The journal of physical chemistry. B.

Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L

Robert S. Germain, Mark Giampapa, Ruhong Zhou, 2006, International Conference on Computational Science.

Accounting for polarization cost when using fixed charge force fields. I. Method for computing energy.

Hans W. Horn, William C Swope, Hans W Horn, 2010, The journal of physical chemistry. B.

Alchemical prediction of hydration free energies for SAMPL

David L. Mobley, Julia E. Rice, William C. Swope, 2012, Journal of Computer-Aided Molecular Design.

Overview of molecular dynamics techniques and early scientific results from the Blue Gene project

Robert S. Germain, Michael Pitman, Frank Suits, 2005, IBM J. Res. Dev..

Toward biodegradable nanogel star polymers via organocatalytic ROP.

J. Hedrick, William Swope, V. Lee, 2012, Chemical communications.

Integrating life sciences data-with a little Garlic

Laura M. Haas, Peter M. Schwarz, Julia E. Rice, 2000, Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering.

DiscoveryLink: A system for integrated access to life sciences data sources

Laura M. Haas, Peter M. Schwarz, Julia E. Rice, 2001, IBM Syst. J..

Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures.

Michael R. Shirts, M. Shirts, V. Pande, 2011, The Journal of chemical physics.

What can digitisation do for formulated product innovation and development?

Michael Johnson, William C. Swope, Richard L. Anderson, 2020 .

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15.

Kyle A. Beauchamp, V. Pande, T. Martínez, 2017, The journal of physical chemistry. B.

Reducing lambda repressor to the core.

Maxim B. Prigozhin, M. Gruebele, William Swope, 2011, The journal of physical chemistry. B.