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Jed W. Pitera - Publications

Affiliations: 
1999 Pharmaceutical Chemistry University of California, San Francisco, San Francisco, CA 
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Year Citation  Score
2014 Pitera JW. Expected distributions of root-mean-square positional deviations in proteins. The Journal of Physical Chemistry. B. 118: 6526-30. PMID 24655018 DOI: 10.1021/Jp412776D  0.325
2014 Lai K, Ozlem M, Pitera JW, Liu CC, Schepis A, Dechene D, Krasnoperova A, Brue D, Abdallah J, Tsai H, Guillorn M, Cheng J, Doerk G, Tjio M, Topalogu R, et al. Computational lithography platform for 193i-guided directed self-assembly Proceedings of Spie - the International Society For Optical Engineering. 9052. DOI: 10.1117/12.2046920  0.31
2012 Pitera JW, Chodera JD. On the Use of Experimental Observations to Bias Simulated Ensembles. Journal of Chemical Theory and Computation. 8: 3445-51. PMID 26592995 DOI: 10.1021/Ct300112V  0.35
2012 Liu CC, Pitera J, Lafferty N, Lai K, Rettner C, Tjio M, Arellano N, Cheng J. Progress towards the integration of optical proximity correction and directed self-assembly of block copolymers with graphoepitaxy Proceedings of Spie - the International Society For Optical Engineering. 8323. DOI: 10.1117/12.916525  0.306
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  0.677
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  0.718
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  0.689
2008 Srinivas G, Pitera JW. Soft patchy nanoparticles from solution-phase self-assembly of binary diblock copolymers. Nano Letters. 8: 611-8. PMID 18189443 DOI: 10.1021/Nl073027Q  0.324
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  0.662
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  0.675
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  0.656
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  0.644
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  0.618
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  0.646
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  0.727
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  0.662
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  0.656
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  0.581
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  0.629
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  0.661
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  0.641
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  0.635
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  0.681
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  0.661
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  0.644
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  0.671
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  0.68
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  0.657
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  0.663
2002 Pitera JW, van Gunsteren WF. A Comparison of Non-Bonded Scaling Approaches for Free Energy Calculations Molecular Simulation. 28: 45-65. DOI: 10.1080/08927020211973  0.336
2001 Pitera JW, Falta M, van Gunsteren WF. Dielectric properties of proteins from simulation: the effects of solvent, ligands, pH, and temperature. Biophysical Journal. 80: 2546-55. PMID 11371433 DOI: 10.1016/S0006-3495(01)76226-1  0.34
2001 Bürgi R, Pitera J, van Gunsteren WF. Assessing the effect of conformational averaging on the measured values of observables. Journal of Biomolecular Nmr. 19: 305-20. PMID 11370777 DOI: 10.1023/A:1011295422203  0.39
2001 Oostenbrink BC, Pitera JW, Meerman JH. Simulations of the estrogen receptor ligand-binding domain: affinity of natural ligands and xenoestrogens. Journal of Medicinal Chemistry. 43: 4594-605. PMID 11101351 DOI: 10.1021/Jm001045D  0.352
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, ... ... Pitera J, 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  0.561
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, ... ... Pitera J, 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  0.649
2000 Pitera JW, Kollman PA. Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides. Proteins. 41: 385-97. PMID 11025549 DOI: 10.1002/1097-0134(20001115)41:3<385::Aid-Prot100>3.0.Co;2-R  0.51
1999 Pitera JW, Munagala NR, Wang CC, Kollman PA. Understanding substrate specificity in human and parasite phosphoribosyltransferases through calculation and experiment. Biochemistry. 38: 10298-306. PMID 10441123 DOI: 10.1021/Bi990250W  0.5
1999 Eriksson MA, Pitera J, Kollman PA. Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations. Journal of Medicinal Chemistry. 42: 868-81. PMID 10072684 DOI: 10.1021/Jm980277Y  0.499
1998 Pitera J, Kollman P. Graphical visualization of mean hydration from molecular dynamics simulations. Journal of Molecular Graphics & Modelling. 15: 355-8, 386-8. PMID 9704297 DOI: 10.1016/S1093-3263(98)00006-0  0.531
1998 Pitera J, Kollman P. Designing an Optimum Guest for a Host Using Multimolecule Free Energy Calculations: Predicting the Best Ligand for Rebek's “Tennis Ball” Journal of the American Chemical Society. 120: 7557-7567. DOI: 10.1021/Ja973028S  0.453
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