Omar Demerdash
Undergraduate education
University of Wisconsin-Madison, BS, 2002
Years in MSTP
2003-2013
PhD
Biophysics, 2010
Mentor
Julie Mitchell, PhD
Thesis title
Modeling of protein function at the intra- and inter-protein level: computational models for allostery hotspot and protein-binding prediction
Postdoctoral fellowship
Chemistry, University of California-Berkeley, 2013-2018
Current position
Liane Russell Distinguished Research Fellow, Oak Ridge National Laboratory, Biosciences Division, Center for Molecular Biophysics
PhD publications
Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A.CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J Mol Biol. 2016 Feb 22;428(4):709-19. PMID: 26854760; PMCID: PMC4794384.
Demerdash ON, Mitchell JC. Density-cluster NMA: A new protein decomposition technique for coarse-grained normal mode analysis. Proteins. 2012 Jul;80(7):1766-79. doi: 10.1002/prot.24072. PMID: 22434479.
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, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol. 2011 Nov 25;414(2):289-302. PMID: 22001016; PMCID: PMC3839241.
Hendrickson ML, Rao AJ, Demerdash ON, Kalil RE. Expression of nestin by neural cells in the adult rat and human brain. PLoS One. 2011 Apr 7;6(4):e18535. PMID: 21490921; PMCID: PMC3072400.
Demerdash ON, Buyan A, Mitchell JC. ReplicOpter: a replicate optimizer for flexible docking. Proteins. 2010 Nov 15;78(15):3156-65. PMID: 20715288.
Demerdash ON, Daily MD, Mitchell JC. Structure-based predictive models for allosteric hot spots. PLoS Comput Biol. 2009 Oct;5(10):e1000531. PMID: 19816556; PMCID: PMC2748687.
Li G, Van Wynsberghe A, Demerdash ONA,Cui Q. Normal mode analysis of macromolecules: From enzyme active sites to molecular machines. In Cui Q, Bahar I (eds.), Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems. Boca Raton, FL: CRC Press. 2006: 65-90.
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. 2013 Nov;81(11):1919-30. PMID: 23760773.
Zhu X, Ericksen SS, Demerdash ON, Mitchell JC. Data driven models for protein interaction and design. Proteins. 2013 Dec;81(12):2221-8. PMID: 24038640.
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, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 2013 Nov;81(11):1980-7. PMID: 23843247; PMCID: PMC4143140.