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Omar N. Demerdash, Ph.D. - Publications

Affiliations: 
2010 University of Wisconsin, Madison, Madison, WI 
Area:
General Biophysics, Molecular Biology
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23 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
2022 Hameedi MA, T Prates E, Garvin MR, Mathews II, Amos BK, Demerdash O, Bechthold M, Iyer M, Rahighi S, Kneller DW, Kovalevsky A, Irle S, Vuong VQ, Mitchell JC, Labbe A, et al. Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Nature Communications. 13: 5285. PMID 36075915 DOI: 10.1038/s41467-022-32922-9  0.501
2021 Hameedi MA, Prates ET, Garvin MR, Mathews I, Kirtley Amos B, Demerdash O, Bechthold M, Iyer M, Rahighi S, Kneller DW, Kovalevsky A, Irle S, Vuong VQ, Mitchell JC, Labbe A, et al. Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Biorxiv : the Preprint Server For Biology. PMID 34816264 DOI: 10.1101/2021.11.11.468228  0.501
2021 Mao Y, Loipersberger M, Horn PR, Das A, Demerdash O, Levine DS, Veccham SP, Head-Gordon T, Head-Gordon M. From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis. Annual Review of Physical Chemistry. PMID 33636998 DOI: 10.1146/annurev-physchem-090419-115149  0.714
2020 Aranha MP, Spooner C, Demerdash O, Czejdo B, Smith JC, Mitchell JC. Prediction of peptide binding to MHC using machine learning with sequence and structure-based feature sets. Biochimica Et Biophysica Acta. General Subjects. 129535. PMID 31954798 DOI: 10.1016/J.Bbagen.2020.129535  0.492
2019 Bortnov V, Tonelli M, Lee W, Lin Z, Annis DS, Demerdash ON, Bateman A, Mitchell JC, Ge Y, Markley JL, Mosher DF. Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum. Nature Communications. 10: 5612. PMID 31819058 DOI: 10.1038/S41467-019-13577-5  0.451
2019 Demerdash O, Shrestha UR, Petridis L, Smith JC, Mitchell JC, Ramanathan A. Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins. Frontiers in Molecular Biosciences. 6: 64. PMID 31475155 DOI: 10.3389/Fmolb.2019.00064  0.537
2018 Das AK, Demerdash ON, Head-Gordon T. Improvements to the AMOEBA Force Field by Introducing Anisotropic Atomic Polarizability of the Water Molecule. Journal of Chemical Theory and Computation. PMID 30428257 DOI: 10.1021/Acs.Jctc.8B00978  0.719
2017 Demerdash O, Mao Y, Liu T, Head-Gordon M, Head-Gordon T. Assessing many-body contributions to intermolecular interactions of the AMOEBA force field using energy decomposition analysis of electronic structure calculations. The Journal of Chemical Physics. 147: 161721. PMID 29096520 DOI: 10.1063/1.4999905  0.623
2017 Demerdash O, Wang L, Head‐Gordon T. Advanced models for water simulations Wires Computational Molecular Science. 8. DOI: 10.1002/Wcms.1355  0.492
2016 Mao Y, Demerdash O, Head-Gordon M, Head-Gordon T. Assessing water-water and water-ion dimer interactions in the AMOEBA force field using energy decomposition analysis of electronic structure calculations. Journal of Chemical Theory and Computation. PMID 27709939 DOI: 10.1021/Acs.Jctc.6B00764  0.609
2016 Albaugh A, Boateng HA, Bradshaw RT, Demerdash ON, Dziedzic J, Mao Y, Margul DT, Swails JM, Zeng Q, Case DA, Eastman PK, Essex JW, Head-Gordon M, Pande VS, Ponder JW, et al. Advanced Potential Energy Surfaces for Molecular Simulation. The Journal of Physical Chemistry. B. PMID 27513316 DOI: 10.1021/Acs.Jpcb.6B06414  0.719
2016 Demerdash ON, Head-Gordon T. Convergence of the Many-Body Expansion for Energy and Forces for Classical Polarizable Models in the Condensed Phase. Journal of Chemical Theory and Computation. PMID 27405002 DOI: 10.1021/Acs.Jctc.6B00335  0.565
2016 Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidmann D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. Journal of Molecular Biology. PMID 26854760 DOI: 10.1016/J.Jmb.2016.01.029  0.536
2015 Albaugh A, Demerdash O, Head-Gordon T. An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction. The Journal of Chemical Physics. 143: 174104. PMID 26547155 DOI: 10.1063/1.4933375  0.708
2014 Demerdash O, Yap EH, Head-Gordon T. Advanced potential energy surfaces for condensed phase simulation Annual Review of Physical Chemistry. 65: 149-174. PMID 24328448 DOI: 10.1146/Annurev-Physchem-040412-110040  0.7
2014 Demerdash O, O'Suilleabhain LD, Head-Gordon TL. Improving the Computational Efficiency of the Induced-Dipole Model in Amoeba via the 3-Body Approximation Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.2295  0.466
2013 Zhu X, Ericksen SS, Demerdash ON, Mitchell JC. Data-driven models for protein interaction and design. Proteins. 81: 2221-8. PMID 24038640 DOI: 10.1002/Prot.24405  0.519
2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... ... Demerdash ON, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356  0.494
2013 Demerdash ON, Mitchell JC. Using physical potentials and learned models to distinguish native binding interfaces from de novo designed interfaces that do not bind. Proteins. 81: 1919-30. PMID 23760773 DOI: 10.1002/Prot.24337  0.553
2012 Demerdash ON, Mitchell JC. Density-cluster NMA: A new protein decomposition technique for coarse-grained normal mode analysis. Proteins. 80: 1766-79. PMID 22434479 DOI: 10.1002/Prot.24072  0.489
2011 Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031  0.523
2010 Demerdash ON, Buyan A, Mitchell JC. ReplicOpter: a replicate optimizer for flexible docking. Proteins. 78: 3156-65. PMID 20715288 DOI: 10.1002/Prot.22811  0.578
2009 Demerdash ON, Daily MD, Mitchell JC. Structure-based predictive models for allosteric hot spots. Plos Computational Biology. 5: e1000531. PMID 19816556 DOI: 10.1371/Journal.Pcbi.1000531  0.521
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