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William C. Swope, Ph.D. - Publications

Affiliations: 
IBM Almaden Research Center, San Jose, CA, United States 
Area:
molecular dynamics, computational chemistry, molecular modeling, statistical mechanics, protein folding, polymer simulation
Website:
http://researcher.watson.ibm.com/researcher/view.php?person=almaden-swope
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53 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Conchuir BO, Gardner K, Jordan KE, Bray DJ, Anderson RL, Johnston MA, Swope WC, Harrison A, Sheehy DR, Peters TJ. An Efficient Algorithm for Topological Characterisation of Worm-Like and Branched Micelle Structures from Simulations. Journal of Chemical Theory and Computation. PMID 32543855 DOI: 10.1021/Acs.Jctc.0C00311  0.405
2019 Swope WC, Johnston MA, Duff AI, McDonagh JL, Anderson RL, Alva G, Tek AT, Maschino AP. The Challenge to Reconcile Experimental Micellar Properties of the CnEm Nonionic Surfactant Family. The Journal of Physical Chemistry. B. PMID 30657322 DOI: 10.1021/Acs.Jpcb.8B11568  0.349
2018 Visscher KM, Swope WC, Geerke DP. A QM/MM Derived Polarizable Water Model for Molecular Simulation. Molecules (Basel, Switzerland). 23. PMID 30501058 DOI: 10.3390/Molecules23123131  0.356
2017 Wang LP, McKiernan KA, Gomes J, Beauchamp KA, Head-Gordon T, Rice JE, Swope WC, Martínez TJ, Pande VS. Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15. The Journal of Physical Chemistry. B. PMID 28306259 DOI: 10.1021/Acs.Jpcb.7B02320  0.653
2016 Johnston MA, Swope WC, Jordan KE, Warren PB, Noro MG, Bray DJ, Anderson RL. Toward a Standard Protocol for Micelle Simulation. The Journal of Physical Chemistry. B. PMID 27096611 DOI: 10.1021/Acs.Jpcb.6B03075  0.434
2012 Vosmeer CR, Rustenburg AS, Rice JE, Horn HW, Swope WC, Geerke DP. QM/MM-Based Fitting of Atomic Polarizabilities for Use in Condensed-Phase Biomolecular Simulation. Journal of Chemical Theory and Computation. 8: 3839-53. PMID 26593025 DOI: 10.1021/Ct300085Z  0.32
2012 Mobley DL, Liu S, Cerutti DS, Swope WC, Rice JE. Alchemical prediction of hydration free energies for SAMPL. Journal of Computer-Aided Molecular Design. 26: 551-62. PMID 22198475 DOI: 10.1007/S10822-011-9528-8  0.343
2011 Prinz JH, Chodera JD, Pande VS, Swope WC, Smith JC, Noé F. Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. The Journal of Chemical Physics. 134: 244108. PMID 21721613 DOI: 10.1063/1.3592153  0.74
2011 Chodera JD, Swope WC, Noé F, Prinz JH, Shirts MR, Pande VS. Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. The Journal of Chemical Physics. 134: 244107. PMID 21721612 DOI: 10.1063/1.3592152  0.793
2011 Prigozhin MB, Sarkar K, Law D, Swope WC, Gruebele M, Pitera J. Reducing lambda repressor to the core. The Journal of Physical Chemistry. B. 115: 2090-6. PMID 21319829 DOI: 10.1021/Jp110175X  0.699
2010 Swope WC, Horn HW, Rice JE. 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. 114: 8631-45. PMID 20540502 DOI: 10.1021/Jp911701H  0.323
2009 Chong LT, Pitera JW, Swope WC, Pande VS. Comparison of computational approaches for predicting the effects of missense mutations on p53 function. Journal of Molecular Graphics & Modelling. 27: 978-82. PMID 19168381 DOI: 10.1016/J.Jmgm.2008.12.006  0.748
2008 Pitera JW, Swope WC, Abraham FF. Observation of noncooperative folding thermodynamics in simulations of 1BBL. Biophysical Journal. 94: 4837-46. PMID 18326644 DOI: 10.1529/Biophysj.107.123265  0.714
2008 Fitch BG, Rayshubskiy A, Eleftheriou M, Ward TJC, Giampapa ME, Pitman Michael C. MC, Pitera JW, Swope WC, Germain RS. Blue matter: Scaling of N-body simulations to one atom per node Ibm Journal of Research and Development. 52: 145-158. DOI: 10.1147/Rd.521.0145  0.692
2008 Fitch BG, Rayshubskiy A, Eleftheriou M, Ward TJC, Giampapa M, Pitman MC, Pitera J, Swope WC, Germain RS. Chapter 6 Blue Matter: Scaling of N-Body Simulations to One Atom per Node Current Topics in Membranes. 60: 159-180. DOI: 10.1016/S1063-5823(08)00006-9  0.701
2007 Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA. Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. Journal of Chemical Theory and Computation. 3: 26-41. PMID 26627148 DOI: 10.1021/Ct0502864  0.757
2007 Srinivas G, Swope WC, Pitera JW. Interfacial fluctuations of block copolymers: a coarse-grain molecular dynamics simulation study. The Journal of Physical Chemistry. B. 111: 13734-42. PMID 18020436 DOI: 10.1021/Jp073347Y  0.669
2007 Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. The Journal of Chemical Physics. 126: 155101. PMID 17461665 DOI: 10.1063/1.2714538  0.734
2007 Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA. Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations Journal of Chemical Theory and Computation. 3: 26-41. DOI: 10.1021/ct0502864  0.73
2006 Pitera JW, Haque I, Swope WC. Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide. The Journal of Chemical Physics. 124: 141102. PMID 16626172 DOI: 10.1063/1.2190226  0.675
2006 Chong LT, Swope WC, Pitera JW, Pande VS. Kinetic computational alanine scanning: application to p53 oligomerization. Journal of Molecular Biology. 357: 1039-49. PMID 16457841 DOI: 10.1016/J.Jmb.2005.12.083  0.755
2006 Chodera JD, Swope WC, Pitera JW, Dill KA. Long-time protein folding dynamics from short-time molecular dynamics simulations Multiscale Modeling and Simulation. 5: 1214-1226. DOI: 10.1137/06065146X  0.756
2006 Larios E, Pitera JW, Swope WC, Gruebele M. Correlation of early orientational ordering of engineered λ6-85 structure with kinetics and thermodynamics Chemical Physics. 323: 45-53. DOI: 10.1016/J.Chemphys.2005.08.048  0.677
2006 Fitch BG, Rayshubskiy A, Eleftheriou M, Ward TJC, Giampapa M, Zhestkov Y, Pitman MC, Suits F, Grossfield A, Pitera J, Swope W, Zhou R, Feller S, Germain RS. Blue matter: Strong scaling of molecular dynamics on Blue Gene/L Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3992: 846-854. DOI: 10.1007/11758525_113  0.614
2005 Horn HW, Swope WC, Pitera JW. Characterization of the TIP4P-Ew water model: vapor pressure and boiling point. The Journal of Chemical Physics. 123: 194504. PMID 16321097 DOI: 10.1063/1.2085031  0.668
2005 Suits F, Pitman MC, Pitera JW, Swope WC, Germain RS. Overview of molecular dynamics techniques and early scientific results from the Blue Gene project Ibm Journal of Research and Development. 49: 475-487. DOI: 10.1147/Rd.492.0475  0.68
2005 Enenkel RF, Fitch BG, Germain RS, Gustavson FG, Martin A, Mendell M, Pitera JW, Pitman MC, Rayshubskiy A, Suits F, Swope WC, Ward TJC. Custom math functions for molecular dynamics Ibm Journal of Research and Development. 49: 465-474. DOI: 10.1147/Rd.492.0465  0.662
2004 Horn HW, Swope WC, Pitera JW, Madura JD, Dick TJ, Hura GL, Head-Gordon T. Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. The Journal of Chemical Physics. 120: 9665-78. PMID 15267980 DOI: 10.1063/1.1683075  0.668
2004 Yang WY, Pitera JW, Swope WC, Gruebele M. Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment. Journal of Molecular Biology. 336: 241-51. PMID 14741219 DOI: 10.1016/J.Jmb.2003.11.033  0.708
2004 Swope WC, Pitera JW, Suits F, Pitman M, Eleftheriou M, Fitch BG, Germain RS, Rayshubski A, Ward TJC, Zhestkov Y, Zhou R. Describing protein folding kinetics by molecular dynamics simulations. 2. Example applications to alanine dipeptide and a β-hairpin peptide Journal of Physical Chemistry B. 108: 6582-6594. DOI: 10.1021/Jp037422Q  0.686
2004 Swope WC, Pitera JW, Suits F, Pitman M, Eleftheriou M, Fitch BG, Germain RS, Rayshubski A, Ward TJC, Zhestkov Y, Zhou R. Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a β-Hairpin Peptide† The Journal of Physical Chemistry B. 108: 6582-6594. DOI: 10.1021/jp037422q  0.673
2004 Swope WC, Pitera JW, Suits F. Describing protein folding kinetics by molecular dynamics simulations. 1. Theory Journal of Physical Chemistry B. 108: 6571-6581. DOI: 10.1021/Jp037421Y  0.7
2003 Pitera JW, Swope W. Understanding folding and design: Replica-exchange simulations of "Trp-cage" miniproteins Proceedings of the National Academy of Sciences of the United States of America. 100: 7587-7592. PMID 12808142 DOI: 10.1073/Pnas.1330954100  0.713
2003 Shirts MR, Pitera JW, Swope WC, Pande VS. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins Journal of Chemical Physics. 119: 5740-5761. DOI: 10.1063/1.1587119  0.777
2003 Fitch BG, Germain RS, Mendell M, Pitera J, Pitman M, Rayshubskiy A, Sham Y, Suits F, Swope W, Ward TJC, Zhestkov Y, Zhou R. Blue Matter, an application framework for molecular simulation on Blue Gene Journal of Parallel and Distributed Computing. 63: 759-773. DOI: 10.1016/S0743-7315(03)00084-4  0.683
2001 Pitman MC, Huber WK, Horn H, Krämer A, Rice JE, Swope WC. FLASHFLOOD: a 3D field-based similarity search and alignment method for flexible molecules. Journal of Computer-Aided Molecular Design. 15: 587-612. PMID 11688943 DOI: 10.1023/A:1011921423829  0.307
2001 Allen F, Almasi G, Andreoni W, Beece D, Berne BJ, Bright A, Brunheroto J, Cascaval C, Castanos J, Coteus P, Crumley P, Curioni A, Denneau M, Donath W, Eleftheriou M, ... ... Swope WC, et al. Blue Gene: A vision for protein science using a petaflop supercomputer Ibm Systems Journal. 40: 310-327. DOI: 10.1147/Sj.402.0310  0.664
2001 Allen F, Almasi G, Andreoni W, Beece D, Berne BJ, Bright A, Brunheroto J, Cascaval C, Castanos J, Coteus P, Crumley P, Curioni A, Denneau M, Donath W, Eleftheriou M, ... ... Swope WC, et al. Blue Gene: A vision for protein science using a petaflop supercomputer Ibm Systems Journal. 40: 310-327. DOI: 10.1147/sj.402.0310  0.582
1996 Bagchi K, Andersen HC, Swope W. Computer simulation study of the melting transition in two dimensions. Physical Review Letters. 76: 255-258. PMID 10061055 DOI: 10.1103/Physrevlett.76.255  0.587
1996 Bagchi K, Andersen HC, Swope W. Observation of a two-stage melting transition in two dimensions. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 53: 3794-3803. PMID 9964691 DOI: 10.1103/Physreve.53.3794  0.499
1995 Swope WC, Andersen HC. A computer simulation method for the calculation of chemical potentials of liquids and solids using the bicanonical ensemble The Journal of Chemical Physics. 102: 2851-2863. DOI: 10.1063/1.468663  0.602
1992 Swope WC, Andersen HC. Thermodynamics, statistical thermodynamics, and computer simulation of crystals with vacancies and interstitials. Physical Review. A. 46: 4539-4548. PMID 9908666 DOI: 10.1103/Physreva.46.4539  0.604
1992 Swope WC, Ferguson DM. Alternative expressions for energies and forces due to angle bending and torsional energy Journal of Computational Chemistry. 13: 585-594. DOI: 10.1002/Jcc.540130508  0.303
1992 Ferguson DM, Pearlman DA, Swope WC, Kollman PA. Free energy perturbation calculations involving potential function changes Journal of Computational Chemistry. 13: 362-370. DOI: 10.1002/Jcc.540130309  0.504
1990 Swope WC, Andersen HC. 10(6)-particle molecular-dynamics study of homogeneous nucleation of crystals in a supercooled atomic liquid. Physical Review. B, Condensed Matter. 41: 7042-7054. PMID 9992961 DOI: 10.1103/Physrevb.41.7042  0.522
1990 Swope WC, Andersen HC. 106-particle molecular-dynamics study of homogeneous nucleation of crystals in a supercooled atomic liquid Physical Review B. 41: 7042-7054. DOI: 10.1103/PhysRevB.41.7042  0.477
1984 Swope WC, Andersen HC. A molecular dynamics method for calculating the solubility of gases in liquids and the hydrophobic hydration of inert-gas atoms in aqueous solution Journal of Physical Chemistry. 88: 6548-6556. DOI: 10.1021/J150670A016  0.539
1983 Andrea TA, Swope WC, Andersen HC. The role of long ranged forces in determining the structure and properties of liquid water The Journal of Chemical Physics. 79: 4576-4584. DOI: 10.1063/1.446373  0.589
1982 Swope WC, Andersen HC, Berens PH, Wilson KR. A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters The Journal of Chemical Physics. 76: 637-649. DOI: 10.1063/1.442716  0.566
1980 Swope WC, Schaefer HF, Yarkony DR. A genealogical electronic coupling procedure incorporating the Hartree-Fock interacting space and suitable for degenerate point groups. Application to excited states of BH3 The Journal of Chemical Physics. 73: 407-415. DOI: 10.1063/1.439889  0.435
1979 Dykstra CE, Swope WC. The H3 + potential surface The Journal of Chemical Physics. 70: 1-3. DOI: 10.1063/1.437223  0.499
1978 Lucchese RR, Brooks BR, Meadows JH, Swope WC, Schaefer HF. BERKELEY: An "open ended" Configuration Interaction (CI) program designed for minicomputers Journal of Computational Physics. 26: 243-251. DOI: 10.1016/0021-9991(78)90095-5  0.371
1977 Dykstra CE, Gaylord AS, Gwinn WD, Swope WC, Schaefer HF. The uncoupled symmetric stretching frequency of H3 + The Journal of Chemical Physics. 68: 3951-3952. DOI: 10.1063/1.436175  0.501
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