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Michael E Wall, Ph.D. - Publications

Affiliations: 
1989-1996 Physics Princeton University, Princeton, NJ 
Area:
X-ray crystallography, diffuse scattering, biophysics, protein dynamics, molecular dynamics simulations
Website:
https://public.lanl.gov/mewall/

37/80 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
2019 Wych DC, Fraser JS, Mobley DL, Wall ME. Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein. Structural Dynamics (Melville, N.Y.). 6: 064704. PMID 31867408 DOI: 10.1063/1.5132692  0.391
2019 Dasgupta M, Budday D, de Oliveira SHP, Madzelan P, Marchany-Rivera D, Seravalli J, Hayes B, Sierra RG, Boutet S, Hunter MS, Alonso-Mori R, Batyuk A, Wierman J, Lyubimov A, Brewster AS, ... ... Wall ME, et al. Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis. Proceedings of the National Academy of Sciences of the United States of America. PMID 31801874 DOI: 10.1073/pnas.1901864116  0.706
2019 Wall ME, CalabrĂ³ G, Bayly CI, Mobley DL, Warren GL. Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations. Journal of the American Chemical Society. PMID 30834751 DOI: 10.1021/Jacs.8B13613  0.346
2019 Wall ME. Save the data! Diffuse scattering to shed light on structural dynamics Acta Crystallographica Section a Foundations and Advances. 75: a49-a49. DOI: 10.1107/S0108767319099501  0.329
2019 Wilson MA, DasGupta M, Su Z, Yoon CH, Wall ME, van den Bedem H. Cysteine modification-gated protein dynamics explored using X-ray diffuse scattering Acta Crystallographica Section a Foundations and Advances. 75: a191-a191. DOI: 10.1107/S0108767319098106  0.436
2019 Wych D, Wall ME, Mobley D. Molecular dynamics simulations of diffuse scattering Acta Crystallographica Section a Foundations and Advances. 75: a247-a247. DOI: 10.1107/S0108767319097575  0.327
2018 Wall ME. Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering. Iucrj. 5: 172-181. PMID 29765607 DOI: 10.1107/S2052252518000519  0.454
2018 Wall ME. Interactions that know no boundaries. Iucrj. 5: 120-121. PMID 29765599 DOI: 10.1107/S2052252518002713  0.309
2018 Wall ME, Wolff AM, Fraser JS. Bringing diffuse X-ray scattering into focus. Current Opinion in Structural Biology. 50: 109-116. PMID 29455056 DOI: 10.1016/J.Sbi.2018.01.009  0.423
2016 Wall ME. Quantum crystallographic charge density of urea. Iucrj. 3: 237-46. PMID 27437111 DOI: 10.1107/S2052252516006242  0.304
2016 Van Benschoten AH, Liu L, Gonzalez A, Brewster AS, Sauter NK, Fraser JS, Wall ME. Measuring and modeling diffuse scattering in protein X-ray crystallography. Proceedings of the National Academy of Sciences of the United States of America. PMID 27035972 DOI: 10.1073/Pnas.1524048113  0.438
2016 Van Benschoten AH, Liu L, Gonzalez A, Brewster AS, Sauter NK, Fraser JS, Wall ME. Measuring and modeling diffuse scattering in protein X-ray crystallography Proceedings of the National Academy of Sciences of the United States of America. 113: 4069-4074. DOI: 10.1073/pnas.1524048113/-/DCSupplemental  0.335
2015 Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams PD, Urzhumtsev A, Fraser JS. Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles. Acta Crystallographica. Section D, Biological Crystallography. 71: 1657-67. PMID 26249347 DOI: 10.1107/S1399004715007415  0.443
2014 Wall ME, Van Benschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering. Proceedings of the National Academy of Sciences of the United States of America. 111: 17887-92. PMID 25453071 DOI: 10.1073/Pnas.1416744111  0.436
2014 Wall ME, Adams PD, Fraser JS, Sauter NK. Diffuse X-ray scattering to model protein motions. Structure (London, England : 1993). 22: 182-4. PMID 24507780 DOI: 10.1016/J.Str.2014.01.002  0.417
2014 Wall ME, Terwilliger TC, Fraser JS, Adams PD, Sauter NK, VanBenschoten A. Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins Biophysical Journal. 106: 384a. DOI: 10.1016/J.Bpj.2013.11.2171  0.461
2012 Verspoor KM, Cohn JD, Ravikumar KE, Wall ME. Text mining improves prediction of protein functional sites. Plos One. 7: e32171. PMID 22393388 DOI: 10.1371/Journal.Pone.0032171  0.326
2012 Ming D, Wall ME. Predicting binding sites by analyzing allosteric effects. Methods in Molecular Biology (Clifton, N.J.). 796: 423-36. PMID 22052504 DOI: 10.1007/978-1-61779-334-9_23  0.337
2009 Wall ME. Methods and software for diffuse X-ray scattering from protein crystals. Methods in Molecular Biology (Clifton, N.J.). 544: 269-79. PMID 19488705 DOI: 10.1007/978-1-59745-483-4_17  0.439
2009 Dreisigmeyer DW, Wall ME. Prediction of Allosteric Linkages in Proteins Biophysical Journal. 96: 573a. DOI: 10.1016/J.Bpj.2008.12.3749  0.347
2009 Cohn JD, Ming D, Wall ME. Prediction of Functional Sites in 50,000 Protein Domains Using Dynamics Perturbation Analysis Biophysical Journal. 96: 650a. DOI: 10.1016/J.Bpj.2008.12.3433  0.369
2008 Ming D, Anghel M, Wall ME. Hidden structure in protein energy landscapes. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 021902. PMID 18352046 DOI: 10.1103/Physreve.77.021902  0.309
2008 Ming D, Cohn JD, Wall ME. Fast dynamics perturbation analysis for prediction of protein functional sites. Bmc Structural Biology. 8: 5. PMID 18234095 DOI: 10.1186/1472-6807-8-5  0.347
2007 Ming D, Wall ME, Sanbonmatsu KY. Domain motions of Argonaute, the catalytic engine of RNA interference. Bmc Bioinformatics. 8: 470. PMID 18053142 DOI: 10.1186/1471-2105-8-470  0.339
2006 Ming D, Wall ME. Interactions in native binding sites cause a large change in protein dynamics. Journal of Molecular Biology. 358: 213-23. PMID 16513135 DOI: 10.1016/J.Jmb.2006.01.097  0.391
2006 Ming D, Wall ME. Erratum: Allostery in a Coarse-Grained Model of Protein Dynamics [Phys. Rev. Lett.95, 198103 (2005)] Physical Review Letters. 96. DOI: 10.1103/Physrevlett.96.159902  0.307
2005 Ming D, Wall ME. Allostery in a coarse-grained model of protein dynamics. Physical Review Letters. 95: 198103. PMID 16384030 DOI: 10.1103/Physrevlett.95.198103  0.3
2005 Ming D, Wall ME. Quantifying allosteric effects in proteins. Proteins. 59: 697-707. PMID 15822100 DOI: 10.1002/Prot.20440  0.338
2003 Wall ME, Francis SH, Corbin JD, Grimes K, Richie-Jannetta R, Kotera J, Macdonald BA, Gibson RR, Trewhella J. Mechanisms associated with cGMP binding and activation of cGMP-dependent protein kinase. Proceedings of the National Academy of Sciences of the United States of America. 100: 2380-5. PMID 12591946 DOI: 10.1073/Pnas.0534892100  0.549
2000 Wall ME, Gallagher SC, Trewhella J. Large-scale shape changes in proteins and macromolecular complexes. Annual Review of Physical Chemistry. 51: 355-80. PMID 11031286 DOI: 10.1146/Annurev.Physchem.51.1.355  0.557
2000 Tung CS, Wall ME, Gallagher SC, Trewhella J. A model of troponin-I in complex with troponin-C using hybrid experimental data: the inhibitory region is a beta-hairpin. Protein Science : a Publication of the Protein Society. 9: 1312-26. PMID 10933496 DOI: 10.1110/Ps.9.7.1312  0.56
1999 Wall ME, Subramaniam S, Phillips GN. Protein structure determination using a database of interatomic distance probabilities. Protein Science : a Publication of the Protein Society. 8: 2720-7. PMID 10631988 DOI: 10.1110/Ps.8.12.2720  0.505
1997 Wall ME, Clarage JB, Phillips GN. Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering Structure. 5: 1599-1612. PMID 9438860 DOI: 10.1016/S0969-2126(97)00308-0  0.723
1997 Wall ME, Ealick SE, Gruner SM. Three-dimensional diffuse x-ray scattering from crystals of Staphylococcal nuclease. Proceedings of the National Academy of Sciences of the United States of America. 94: 6180-4. PMID 9177191 DOI: 10.1073/Pnas.94.12.6180  0.557
1996 Wall ME, Gruner SM, Ealick SE. Three-dimensional diffuse X-ray scattering from staphylococcal nuclease Acta Crystallographica Section a Foundations of Crystallography. 52: C16-C16. DOI: 10.1107/S0108767396098352  0.559
1995 Walter RL, Thiel DJ, Barna SL, Tate MW, Wall ME, Eikenberry EF, Gruner SM, Ealick SE. High-resolution macromolecular structure determination using CCD detectors and synchrotron radiation. Structure (London, England : 1993). 3: 835-44. PMID 7582900 DOI: 10.1016/S0969-2126(01)00218-0  0.693
1995 Tate MW, Eikenberry EF, Barna SL, Wall ME, Lowrance JL, Gruner SM. A Large-Format High-Resolution Area X-ray Detector Based on a Fiber-Optically Bonded Charge-Coupled Device (CCD) Journal of Applied Crystallography. 28: 196-205. DOI: 10.1107/S0021889894007867  0.7
Low-probability matches (unlikely to be authored by this person)
2021 Su Z, Dasgupta M, Poitevin F, Mathews II, van den Bedem H, Wall ME, Yoon CH, Wilson MA. Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters. Structural Dynamics (Melville, N.Y.). 8: 044701. PMID 34258328 DOI: 10.1063/4.0000087  0.296
2008 Cohn JD, Ming D, Wall ME. Prediction of Functional Sites in SCOP Domains using Dynamics Perturbation Analysis Nature Precedings. 3: 1-1. DOI: 10.1038/Npre.2008.2209.1  0.296
2016 Negre CF, Mniszewski SM, Cawkwell MJ, Bock N, Wall ME, Niklasson AM. Recursive Factorization of the Inverse Overlap Matrix in Linear Scaling Quantum Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 27267207 DOI: 10.1021/Acs.Jctc.6B00154  0.295
2009 Wall ME, Markowitz DA, Rosner JL, Martin RG. Model of transcriptional activation by MarA in Escherichia coli. Plos Computational Biology. 5: e1000614. PMID 20019803 DOI: 10.1371/Journal.Pcbi.1000614  0.286
2012 Ravikumar K, Liu H, Cohn JD, Wall ME, Verspoor K. Literature mining of protein-residue associations with graph rules learned through distant supervision. Journal of Biomedical Semantics. 3: S2. PMID 23046792 DOI: 10.1186/2041-1480-3-S3-S2  0.286
2007 Edwards JS, Faeder JR, Hlavacek WS, Jiang Y, Nemenman I, Wall ME. Q-bio 2007: a watershed moment in modern biology. Molecular Systems Biology. 3: 148. PMID 18059443 DOI: 10.1038/Msb4100193  0.284
2023 Wych DC, Wall ME. Molecular-dynamics simulations of macromolecular diffraction, part I: Preparation of protein crystal simulations. Methods in Enzymology. 688: 87-114. PMID 37748833 DOI: 10.1016/bs.mie.2023.06.008  0.277
2023 Wych DC, Wall ME. Molecular-dynamics simulations of macromolecular diffraction, part II: Analysis of protein crystal simulations. Methods in Enzymology. 688: 115-143. PMID 37748824 DOI: 10.1016/bs.mie.2023.06.012  0.273
2023 Young ID, Mendez D, Poon BK, Blaschke JP, Wittwer F, Wall ME, Sauter NK. Interpreting macromolecular diffraction through simulation. Methods in Enzymology. 688: 195-222. PMID 37748827 DOI: 10.1016/bs.mie.2023.06.011  0.272
2024 Smith N, Dasgupta M, Wych DC, Dolamore C, Sierra RG, Lisova S, Marchany-Rivera D, Cohen AE, Boutet S, Hunter MS, Kupitz C, Poitevin F, Moss FR, Mittan-Moreau DW, Brewster AS, ... ... Wall ME, et al. Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography. Science Advances. 10: eadk7201. PMID 38536910 DOI: 10.1126/sciadv.adk7201  0.267
2016 Vesselinova N, Alexandrov BS, Wall ME. Dynamical Model of Drug Accumulation in Bacteria: Sensitivity Analysis and Experimentally Testable Predictions. Plos One. 11: e0165899. PMID 27824914 DOI: 10.1371/Journal.Pone.0165899  0.266
2014 Phillips JL, Ganguly K, Wren M, Gupta G, Wall ME, Gnanakaran S. Systems Level Study of Bacterial Multi-Drug Resistance from Efflux Machinery Biophysical Journal. 106: 791a. DOI: 10.1016/J.Bpj.2013.11.4336  0.263
2011 Wall ME. Structure-function relations are subtle in genetic regulatory networks. Mathematical Biosciences. 231: 61-8. PMID 21329703 DOI: 10.1016/J.Mbs.2011.02.003  0.262
2003 Wall ME, Hlavacek WS, Savageau MA. Design principles for regulator gene expression in a repressible gene circuit. Journal of Molecular Biology. 332: 861-76. PMID 12972257 DOI: 10.1016/S0022-2836(03)00948-3  0.261
2023 Wych DC, Aoto PC, Vu L, Wolff AM, Mobley DL, Fraser JS, Taylor SS, Wall ME. Molecular-dynamics simulation methods for macromolecular crystallography. Acta Crystallographica. Section D, Structural Biology. 79: 50-65. PMID 36601807 DOI: 10.1107/S2059798322011871  0.261
2015 Mniszewski SM, Cawkwell MJ, Wall ME, Mohd-Yusof J, Bock N, Germann TC, Niklasson AM. Efficient Parallel Linear Scaling Construction of the Density Matrix for Born-Oppenheimer Molecular Dynamics. Journal of Chemical Theory and Computation. 11: 4644-54. PMID 26574255 DOI: 10.1021/Acs.Jctc.5B00552  0.26
2023 Smith N, Dasgupta M, Wych DC, Dolamore C, Sierra RG, Lisova S, Marchany-Rivera D, Cohen AE, Boutet S, Hunter MS, Kupitz C, Poitevin F, Moss FR, Brewster AS, Sauter NK, ... ... Wall ME, et al. Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography. Biorxiv : the Preprint Server For Biology. PMID 37645800 DOI: 10.1101/2023.08.15.553460  0.26
2008 Dreisigmeyer DW, Stajic J, Nemenman I, Hlavacek WS, Wall ME. Determinants of bistability in induction of the Escherichia coli lac operon. Iet Systems Biology. 2: 293-303. PMID 19045824 DOI: 10.1049/Iet-Syb:20080095  0.258
2011 Dunbar J, Cohn JD, Wall ME. Consistency of gene starts among Burkholderia genomes. Bmc Genomics. 12: 125. PMID 21342528 DOI: 10.1186/1471-2164-12-125  0.257
2005 Wall ME, Dunlop MJ, Hlavacek WS. Multiple functions of a feed-forward-loop gene circuit. Journal of Molecular Biology. 349: 501-14. PMID 15890368 DOI: 10.1016/J.Jmb.2005.04.022  0.254
2001 Wall ME, Dyck PA, Brettin TS. SVDMAN--singular value decomposition analysis of microarray data. Bioinformatics (Oxford, England). 17: 566-8. PMID 11395437 DOI: 10.1093/Bioinformatics/17.6.566  0.254
2016 Niklasson AM, Mniszewski SM, Negre CF, Cawkwell MJ, Swart PJ, Mohd-Yusof J, Germann TC, Wall ME, Bock N, Rubensson EH, Djidjev H. Graph-based linear scaling electronic structure theory. The Journal of Chemical Physics. 144: 234101. PMID 27334148 DOI: 10.1063/1.4952650  0.252
2008 Martin RG, Bartlett ES, Rosner JL, Wall ME. Activation of the Escherichia coli marA/soxS/rob regulon in response to transcriptional activator concentration. Journal of Molecular Biology. 380: 278-84. PMID 18514222 DOI: 10.1016/J.Jmb.2008.05.015  0.249
2011 Nemenman I, Faeder JR, Hlavacek WS, Jiang Y, Wall ME, Zilman A. Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing. Physical Biology. 8: 050301. PMID 21832800 DOI: 10.1088/1478-3975/8/5/050301  0.244
2014 Ganguly K, Phillips J, Wren M, Pardington P, Gnanakaran S, Wall M, Gupta G. Interdependence of multi-drug efflux pumps and quorum sensing systems in Pseudomonas aeruginosa International Journal of Infectious Diseases. 21: 92. DOI: 10.1016/J.Ijid.2014.03.620  0.241
2007 Nemenman I, Escola GS, Hlavacek WS, Unkefer PJ, Unkefer CJ, Wall ME. Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism. Annals of the New York Academy of Sciences. 1115: 102-15. PMID 17925356 DOI: 10.1196/Annals.1407.013  0.234
2011 Wall ME, Raghavan S, Cohn JD, Dunbar J. Genome majority vote improves gene predictions. Plos Computational Biology. 7: e1002284. PMID 22131910 DOI: 10.1371/Journal.Pcbi.1002284  0.23
2004 Wall ME, Hlavacek WS, Savageau MA. Design of gene circuits: lessons from bacteria. Nature Reviews. Genetics. 5: 34-42. PMID 14708014 DOI: 10.1038/Nrg1244  0.216
2009 Nemenman I, Wall M, Hlavacek W, Jiang Y. Editorial: Selected papers from the Second q-bio Conference on Cellular Information Processing Iet Systems Biology. 3: 297-299. DOI: 10.1049/Iet-Syb.2009.9045  0.208
2010 Nemenman I, Hlavacek WS, Jiang Y, Wall ME, Zilman A. The Third q-bio Conference on Cellular Information Processing. Iet Systems Biology. 4: 331-3. PMID 21073232 DOI: 10.1049/Iet-Syb.2010.9133  0.207
2008 Nemenman I, Hlavacek WS, Edwards JS, Faeder JR, Jiang Y, Wall ME. Selected papers from the First q-bio Conference on Cellular Information Processing. Iet Systems Biology. 2: 203-5. PMID 19045816 DOI: 10.1049/Iet-Syb:20089018  0.2
2014 Nemenman I, Faeder JR, Gnanakaran S, Hlavacek WS, Munsky B, Wall ME, Jiang Y. The Seventh q-bio Conference: meeting report and preface. Physical Biology. 11: 040301. PMID 25075709 DOI: 10.1088/1478-3975/11/4/040301  0.199
2013 Nemenman I, Gnanakaran S, Munsky B, Wall ME, Jiang Y, Hlavacek WS, Faeder JR. Special section dedicated to The Sixth q-bio Conference: meeting report and preface. Physical Biology. 10: 030301. PMID 23735417 DOI: 10.1088/1478-3975/10/3/030301  0.194
2015 Hlavacek WS, Gnanakaran S, Munsky B, Wall ME, Faeder JR, Jiang Y, Nemenman I, Resnekov O. The eighth q-bio conference: meeting report and special issue preface. Physical Biology. 12: 060401. PMID 26716953 DOI: 10.1088/1478-3975/12/6/060401  0.192
2012 Nemenman I, Gnanakaran S, Hlavacek WS, Jiang Y, Munsky B, Wall ME, Faeder JR. The Fifth Annual q-bio Conference on Cellular Information Processing Physical Biology. 9. DOI: 10.1088/1478-3975/9/5/050201  0.183
2013 Verspoor K, Mackinlay A, Cohn JD, Wall ME. Detection of protein catalytic sites in the biomedical literature. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 433-44. PMID 23424147  0.182
2023 Doyle MD, Bhowmick A, Wych DC, Lassalle L, Simon PS, Holton J, Sauter NK, Yachandra VK, Kern JF, Yano J, Wall ME. Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography. Journal of the American Chemical Society. PMID 37369071 DOI: 10.1021/jacs.3c01412  0.176
2022 Ge Y, Wych DC, Samways ML, Wall ME, Essex JW, Mobley DL. Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques. Journal of Chemical Theory and Computation. PMID 35148093 DOI: 10.1021/acs.jctc.1c00590  0.164
2011 Ravikumar KE, Liu H, Cohn JD, Wall ME, Verspoor K. Pattern learning through distant supervision for extraction of protein-residue associations in the biomedical literature Proceedings - 10th International Conference On Machine Learning and Applications, Icmla 2011. 2: 59-65. DOI: 10.1109/ICMLA.2011.112  0.161
2025 Cavender CE, Case DA, Chen JC, Chong LT, Keedy DA, Lindorff-Larsen K, Mobley DL, Ollila OHS, Oostenbrink C, Robustelli P, Voelz VA, Wall ME, Wych DC, Gilson MK. Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields. Arxiv. PMID 40196146  0.154
2023 Negre CFA, Wall ME, Niklasson AMN. Graph-based quantum response theory and shadow Born-Oppenheimer molecular dynamics. The Journal of Chemical Physics. 158: 074108. PMID 36813723 DOI: 10.1063/5.0137119  0.142
2024 Fattebert JL, Negre CFA, Finkelstein J, Mohd-Yusof J, Osei-Kuffuor D, Wall ME, Zhang Y, Bock N, Mniszewski SM. Hybrid programming-model strategies for GPU offloading of electronic structure calculation kernels. The Journal of Chemical Physics. 160. PMID 38551311 DOI: 10.1063/5.0198797  0.103
2018 Tuohy JM, Mueller-Spitz SR, Albert CM, Scholz-Ng SE, Wall ME, Noutsios GT, Gutierrez AJ, Sandrin TR. MALDI-TOF MS Affords Discrimination of Isolates Obtained From Diverse Biofilm Habitats. Frontiers in Microbiology. 9: 2442. PMID 30374340 DOI: 10.3389/Fmicb.2018.02442  0.058
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