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Michael J. Schnieders, D.Sc. - Publications

Affiliations: 
2007 Washington University, Saint Louis, St. Louis, MO 
Area:
General Biophysics, Condensed Matter Physics, Biomedical Engineering
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37 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
2024 Thiel AC, Speranza MJ, Jadhav S, Stevens LL, Unruh DK, Ren P, Ponder JW, Shen J, Schnieders MJ. Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of Chemical Theory and Computation. PMID 38507252 DOI: 10.1021/acs.jctc.3c01180  0.695
2023 Corrigan RA, Thiel AC, Lynn JR, Casavant TL, Ren P, Ponder JW, Schnieders MJ. A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model. The Journal of Chemical Physics. 159. PMID 37526158 DOI: 10.1063/5.0158914  0.732
2021 Corrigan RA, Qi G, Thiel AC, Lynn JR, Walker BD, Casavant TL, Lagardere L, Piquemal JP, Ponder JW, Ren P, Schnieders MJ. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. Journal of Chemical Theory and Computation. PMID 33769814 DOI: 10.1021/acs.jctc.0c01286  0.748
2019 Tollefson MR, Litman JM, Qi G, O'Connell CE, Wipfler MJ, Marini RJ, Bernabe HV, Tollefson WTA, Braun TA, Casavant TL, Smith RJH, Schnieders MJ. Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking. Biophysical Journal. PMID 31327459 DOI: 10.1016/J.Bpj.2019.06.030  0.421
2019 Litman J, Thiel AC, Schnieders MJ. Scalable Indirect Free Energy Method Applied to Divalent Cation-Metalloprotein Binding. Journal of Chemical Theory and Computation. PMID 31268700 DOI: 10.1021/Acs.Jctc.9B00147  0.496
2018 Rackers JA, Wang Z, Lu C, Laury ML, Lagardère L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW. Tinker 8: Software Tools for Molecular Design. Journal of Chemical Theory and Computation. 14: 5273-5289. PMID 30176213 DOI: 10.1021/Acs.Jctc.8B00529  0.723
2018 Lagardère L, Jolly LH, Lipparini F, Aviat F, Stamm B, Jing ZF, Harger M, Torabifard H, Cisneros GA, Schnieders MJ, Gresh N, Maday Y, Ren PY, Ponder JW, Piquemal JP. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chemical Science. 9: 956-972. PMID 29732110 DOI: 10.1039/C7Sc04531J  0.733
2017 Avdic A, Tollefson MR, Tatro N, LuCore SD, Litman JM, Fenn TD, Schnieders MJ. Polarizable Amoeba Force Field Metadynamics with Minimization Predicts Missing Protein Loops Biophysical Journal. 112: 55a. DOI: 10.1016/J.Bpj.2016.11.332  0.493
2016 Nessler IJ, Litman JM, Schnieders MJ. Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals. Physical Chemistry Chemical Physics : Pccp. PMID 27524378 DOI: 10.1039/C6Cp02595A  0.496
2016 Bell DR, Qi R, Jing Z, Xiang JY, Mejias C, Schnieders MJ, Ponder JW, Ren P. Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field. Physical Chemistry Chemical Physics : Pccp. PMID 27254477 DOI: 10.1039/C6Cp02509A  0.721
2016 Litman JM, Joo Sun Y, Hou T, LuCore SD, Panel N, Simonson T, Fuentes EJ, Schnieders MJ. Protein Sequence Optimization with a Polarizable Force Field: Insights from PDZ Domains Biophysical Journal. 110: 345a-346a. DOI: 10.1016/J.Bpj.2015.11.1859  0.449
2015 Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP. Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle mesh Ewald. Journal of Chemical Theory and Computation. 11: 2589-99. PMID 26575557 DOI: 10.1021/Acs.Jctc.5B00171  0.641
2015 Lipparini F, Lagardère L, Raynaud C, Stamm B, Cancès E, Mennucci B, Schnieders M, Ren P, Maday Y, Piquemal JP. Polarizable molecular dynamics in a polarizable continuum solvent. Journal of Chemical Theory and Computation. 11: 623-34. PMID 26516318 DOI: 10.1021/Ct500998Q  0.627
2015 LuCore SD, Litman JM, Powers KT, Gao S, Lynn AM, Tollefson WT, Fenn TD, Washington MT, Schnieders MJ. Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures. Biophysical Journal. 109: 816-26. PMID 26287633 DOI: 10.1016/J.Bpj.2015.06.062  0.497
2014 Park J, Nessler I, McClain B, Macikenas D, Baltrusaitis J, Schnieders MJ. Absolute Organic Crystal Thermodynamics: Growth of the Asymmetric Unit into a Crystal via Alchemy. Journal of Chemical Theory and Computation. 10: 2781-91. PMID 26586507 DOI: 10.1021/Ct500180M  0.406
2014 Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP. Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald. Journal of Chemical Theory and Computation. 10: 1638-1651. PMID 26512230 DOI: 10.1021/Ct401096T  0.641
2014 LuCore SD, Gao S, Lynn AM, Tollefson WT, Powers KT, Fenn TD, Schnieders MJ. Biomolecular Structure Refinement & Prediction using Dead-End Elimination with a Polarizable Force Field Biophysical Journal. 106: 407a. DOI: 10.1016/J.Bpj.2013.11.2294  0.481
2012 Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M, Zhang J, Baker NA. Biomolecular electrostatics and solvation: a computational perspective. Quarterly Reviews of Biophysics. 45: 427-91. PMID 23217364 DOI: 10.1017/S003358351200011X  0.59
2012 Schnieders MJ, Baltrusaitis J, Shi Y, Chattree G, Zheng L, Yang W, Ren P. The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field. Journal of Chemical Theory and Computation. 8: 1721-1736. PMID 22582032 DOI: 10.1021/Ct300035U  0.626
2012 Schnieders MJ, Kaoud TS, Yan C, Dalby KN, Ren P. Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases. Current Pharmaceutical Design. 18: 1173-85. PMID 22316156 DOI: 10.2174/138920012799362873  0.487
2012 Schnieders MJ, Shi Y, Wu J, Baltrusaitis J, Yang W, Ren P. Pharmaceutical Applications of the Polarizable Amoeba Potential, Including Protein-Ligand Binding Affinity and Drug Solubility, using the Force Field X Software Biophysical Journal. 102: 409a-410a. DOI: 10.1016/J.Bpj.2011.11.2239  0.665
2012 Fenn T, Schnieders M, Pande V. Bayesian Modeling of Crystallographic Disorder Biophysical Journal. 102: 225a. DOI: 10.1016/J.Bpj.2011.11.1235  0.381
2011 Schnieders MJ, Fenn TD, Pande VS. Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals. Journal of Chemical Theory and Computation. 7: 1141-1156. PMID 26606362 DOI: 10.1021/Ct100506D  0.429
2011 Fenn TD, Schnieders MJ. Polarizable atomic multipole X-ray refinement: weighting schemes for macromolecular diffraction. Acta Crystallographica. Section D, Biological Crystallography. 67: 957-65. PMID 22101822 DOI: 10.1107/S0907444911039060  0.372
2011 MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill KA. Assessment of protein structure refinement in CASP9. Proteins. 79: 74-90. PMID 22069034 DOI: 10.1002/Prot.23131  0.347
2011 Fenn TD, Schnieders MJ, Mustyakimov M, Wu C, Langan P, Pande VS, Brunger AT. Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration. Structure (London, England : 1993). 19: 523-33. PMID 21481775 DOI: 10.1016/J.Str.2011.01.015  0.389
2010 Fenn TD, Schnieders MJ, Brunger AT. A smooth and differentiable bulk-solvent model for macromolecular diffraction. Acta Crystallographica. Section D, Biological Crystallography. 66: 1024-31. PMID 20823553 DOI: 10.1107/S0907444910031045  0.412
2010 Fenn TD, Schnieders MJ, Brunger AT, Pande VS. Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules. Biophysical Journal. 98: 2984-92. PMID 20550911 DOI: 10.1016/J.Bpj.2010.02.057  0.497
2010 Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GN, Johnson ME, Head-Gordon T. Current status of the AMOEBA polarizable force field. The Journal of Physical Chemistry. B. 114: 2549-64. PMID 20136072 DOI: 10.1021/Jp910674D  0.76
2010 Schnieders MJ, Fenn TD, Pande VS, Brunger AT. X-Ray Crystallography Refinement as Ewald Intended: From Drug Design to Ribosome Crystals Biophysical Journal. 98: 177a. DOI: 10.1016/J.Bpj.2009.12.946  0.424
2010 Fenn T, Schnieders M, Pande V, Brunger A. Is Theory Leading Neutron Diffraction in Macromolecular Solvent Networks? Biophysical Journal. 98: 760a. DOI: 10.1016/J.Bpj.2009.12.4172  0.398
2009 Shi Y, Jiao D, Schnieders MJ, Ren P. Trypsin-ligand binding free energy calculation with AMOEBA. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 2328-31. PMID 19965178 DOI: 10.1109/IEMBS.2009.5335108  0.526
2009 MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA. Assessment of the protein-structure refinement category in CASP8. Proteins. 77: 66-80. PMID 19714776 DOI: 10.1002/Prot.22538  0.335
2009 Schnieders MJ, Fenn TD, Pande VS, Brunger AT. Polarizable atomic multipole X-ray refinement: application to peptide crystals. Acta Crystallographica. Section D, Biological Crystallography. 65: 952-65. PMID 19690373 DOI: 10.1107/S0907444909022707  0.443
2009 Jiao D, Zhang J, Duke RE, Li G, Schnieders MJ, Ren P. Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. Journal of Computational Chemistry. 30: 1701-11. PMID 19399779 DOI: 10.1002/Jcc.21268  0.602
2007 Schnieders MJ, Ponder JW. Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum. Journal of Chemical Theory and Computation. 3: 2083-97. PMID 26636202 DOI: 10.1021/Ct7001336  0.715
2007 Schnieders MJ, Baker NA, Ren P, Ponder JW. Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. The Journal of Chemical Physics. 126: 124114. PMID 17411115 DOI: 10.1063/1.2714528  0.747
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