Publications

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ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes.
Borrman T, Cimons J, Cosiano M, Purcaro M, Pierce BG, Baker BM, Weng Z. 2017. ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes. Proteins 85(5): 908-916. DOI: 10.1002/prot.25260
TumbleScore: Run and tumble analysis for low frame-rate motility videos.
Pottash AE, McKay R, Virgile CR, Ueda H, Bentley WE. 2017. TumbleScore: Run and tumble analysis for low frame-rate motility videos. BioTechniques 62(1): 31-36. DOI: 10.2144/000114493
DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase.
Li H, Endutkin AV, Bergonzo C, Fu L, Grollman A, Zharkov DO, Simmerling C. 2017. DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase. Journal of the American Chemical Society 139(7): 2682-2692. DOI: 10.1021/jacs.6b11433
Electronic control of gene expression and cell behaviour in Escherichia coli through redox signalling.
Tschirhart T, Kim E, McKay R, Ueda H, Wu HC, Pottash AE, Zargar A, Negrete A, Shiloach J, Payne GF, et al. 2017. Electronic control of gene expression and cell behaviour in Escherichia coli through redox signalling. Nature communications 8: 14030. DOI: 10.1038/ncomms14030
Fast formation of low-defect-density tethered bilayers by fusion of multilamellar vesicles.
Ragaliauskas T, Mickevicius M, Rakovska B, Penkauskas T, Vanderah DJ, Heinrich F, Valincius G. 2017. Fast formation of low-defect-density tethered bilayers by fusion of multilamellar vesicles. Biochimica et biophysica acta. Biomembranes 1859(5): 669-678. DOI: 10.1016/j.bbamem.2017.01.015
Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology.
Li J, Liu Y, Kim E, March JC, Bentley WE, Payne GF. 2017. Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology. Free radical biology & medicine 105: 110-131. DOI: 10.1016/j.freeradbiomed.2016.12.029
Redox Probing for Chemical Information of Oxidative Stress.
Kim E, Winkler TE, Kitchen C, Kang M, Banis G, Bentley WE, Kelly DL, Ghodssi R, Payne GF. 2017. Redox Probing for Chemical Information of Oxidative Stress. Analytical chemistry 89(3): 1583-1592. DOI: 10.1021/acs.analchem.6b03620
Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons.
Lin J, Pozharski E, Wilson MA. 2017. Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons. Biochemistry 56(2): 391-402. DOI: 10.1021/acs.biochem.6b00906
Mathematical model of LsrR-binding and derepression in Escherichia coli K12.
Graff SM, Bentley WE. 2017. Mathematical model of LsrR-binding and derepression in Escherichia coli K12. Journal of bioinformatics and computational biology 15(1): 1650039. DOI: 10.1142/S0219720016500396
Insightful directed evolution of Escherichia coli quorum sensing promoter region of the lsrACDBFG operon: a tool for synthetic biology systems and protein expression.
Hauk P, Stephens K, Mckay R, Virgile CR, Ueda H, Ostermeier M, Ryu KS, Sintim HO, Bentley WE. 2016. Insightful directed evolution of Escherichia coli quorum sensing promoter region of the lsrACDBFG operon: a tool for synthetic biology systems and protein expression. Nucleic acids research 44(21): 10515-10525.
Cellular aspartyl proteases promote the unconventional secretion of biologically active HIV-1 matrix protein p17.
Caccuri F, Iaria ML, Campilongo F, Varney K, Rossi A, Mitola S, Schiarea S, Bugatti A, Mazzuca P, Giagulli C, et al. 2016. Cellular aspartyl proteases promote the unconventional secretion of biologically active HIV-1 matrix protein p17. Scientific reports 6: 38027. DOI: 10.1038/srep38027
The Expanding Role of the BCL6 Oncoprotein as a Cancer Therapeutic Target.
Cardenas MG, Oswald E, Yu W, Xue F, MacKerell AD, Melnick AM. 2017. The Expanding Role of the BCL6 Oncoprotein as a Cancer Therapeutic Target. Clinical cancer research : an official journal of the American Association for Cancer Research 23(4): 885-893. DOI: 10.1158/1078-0432.CCR-16-2071
Computer-Aided Drug Design Methods.
Yu W, MacKerell AD. 2017. Computer-Aided Drug Design Methods. Methods in molecular biology (Clifton, N.J.) 1520: 85-106. DOI: 10.1007/978-1-4939-6634-9_5
Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data.
Ying J, Delaglio F, Torchia DA, Bax A. 2017. Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data. Journal of biomolecular NMR 68(2): 101-118. DOI: 10.1007/s10858-016-0072-7
Homologues of the RPW8 Resistance Protein Are Localized to the Extrahaustorial Membrane that Is Likely Synthesized De Novo.
Berkey R, Zhang Y, Ma X, King H, Zhang Q, Wang W, Xiao S. 2017. Homologues of the RPW8 Resistance Protein Are Localized to the Extrahaustorial Membrane that Is Likely Synthesized De Novo. Plant physiology 173(1): 600-613. DOI: 10.1104/pp.16.01539