Tidor Lab Publications

	Rational approaches to improving selectivity in drug design. D. J. Huggins, W. Sherman, and B. Tidor. J. Med. Chem. 55: 1424-1444 (2012).
	Efficient calculation of molecular configurational entropies using an information theoretic approximation. B. M. King, N. W. Silver, and B. Tidor. J. Phys. Chem. B 116: 2891-2904 (2012).
	Exploring the gap between dynamic and constraint-based models of metabolism. D. Machado, R. S. Costa, E. C. Ferreira, I. Rocha, and B. Tidor. Metab. Eng. 14: 112-119 (2012).
	Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance. M. K. Parai, D. J. Huggins, H. Cao, M. N. Nalam, A. Ali, C. A. Schiffer, B. Tidor, and T. M. Rana. J. Med. Chem. 55: 6328-6341 (2012).
	Charge Optimization Theory for Induced-Fit Ligands. Y. Shen, M. K. Gilson, and B.Tidor. J. Chem. Theory Comput. 8: 4580-4592 (2012).
	Reply to Comment on "Sloppy models, parameter uncertainty, and the role of experimental design". D. R. Hagen, J. F. Apgar, D. K. Witmer, F. M. White, and B. Tidor. Mol. Biosyst. 7: 2523-2524 (2011).
	An integrated mathematical model of thrombin-, histamine-and VEGF-mediated signalling in endothelial permeability. X. N. Wei, B. C. Han, J. X. Zhang, X. H. Liu, C. Y. Tan, Y. Y. Jiang, B. C. Low, B. Tidor, and Y. Z. Chen. BMC Syst. Biol. 5: 112 (2011).
	Simulating EGFR-ERK signaling control by scaffold proteins KSR and MP1 reveals differential ligand-sensitivity co-regulated by Cbl-CIN85 and endophilin. L. Huang, C. Q. Pan, B. Li, L. Tucker-Kellogg, B. Tidor, Y. Chen, and B. C. Low. PLoS One 6: e22933 (2011).
	Systematic placement of structural water molecules for improved scoring of protein-ligand interactions. D. J. Huggins and B. Tidor. Protein Eng. Des. Sel. 24: 777-789 (2011).
	Delineation of lipopolysaccharide (LPS)-binding sites on hemoglobin: From in silico predictions to biophysical characterization. N. Bahl, R. Du, I. Winarsih, B. Ho, L. Tucker-Kellogg, B. Tidor, and J. L. Ding. J. Biol. Chem. 28: 37793-37803 (2011).
	Modeling formalisms in systems biology. D. Machado, R. S. Cost, M. Rocha, E. C. Ferreira, B. Tidor, and I. Rocha. A.M.B. Express 45:(2011).
	Evaluating the substrate-envelope hypothesis: Structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. M. N. Nalam, A. Ali, M. D. Altman, G. S. Reddy, S. Chellappan, V. Kairys, A. Ozen, H. Cao, M. K. Gilson, B. Tidor, T. M. Rana, and C. A. Schiffer. J. Virol. 84: 5368-5378 (2010).
	Sloppy models, parameter uncertainty, and the role of experimental design. J .F. Apgar, D. K. Witmer, F. M. White, and B. Tidor. Mol. Biosyst. 6: 1890-1900 (2010).
	Cellular level models as tools for cytokine design. M. L. Radhakrishnan and B. Tidor. Biotechnol. Prog. 26: 919-937 (2010).
	Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. E. Leonard, P. K. Ajikumar, K. Thayer, W. H. Xiao, J. D. Mo, B. Tidor, G. Stephanopoulos, and K. L. Prather. Proc. Natl. Acad. Sci. U.S.A. 107: 1365-13659 (2010).
	Evaluation of an inverse molecular design algorithm in a model binding site. D. J. Huggins, M. D. Altman, and B. Tidor. Proteins: Struct., Funct., Bioinf. 75: 168-186 (2009).
	Rotamer optimization for protein design through MAP estimation and problem-size reduction. E. J. Hong, S. M. Lippow, B. Tidor, and T. Lozano-Pérez. J. Comput. Chem. 30: 1923-1945 (2009).
	Distinct mechanisms act in concert to mediate cell cycle arrest. J. E. Toettcher, A. Loewer, G. J. Ostheimer, M. B. Yaffe, B. Tidor, and G. Lahav. Proc. Natl. Acad. Sci. U.S.A. 106: 785-790 (2009).
	Symmetric signaling by an asymmetric 1 erythropoietin: 2 erythropoietin receptor complex. Y. L. Zhang, M. L. Radhakrishnan, X. Lu, A. W. Gross, B. Tidor, and H. F. Lodish. Mol. Cell 33: 266-274 (2009).
	Additivity in the analysis and design of HIV protease inhibitors. R. N. Jorissen, G. S. Reddy, A. Ali, M. D. Altman, S. Chellappan, S. G. Anjum, B. Tidor, C. A. Schiffer, T. M. Rana, and M. K. Gilson. J. Med. Chem. 52: 737-754 (2009).
	MIST: Maximum information spanning trees for dimension reduction of biological data sets. B. M. King and B. Tidor. Bioinformatics 25: 1165-1172 (2009).
	Synergistic drug-cytokine induction of hepatocellular death as an in vitro approach for the study of inflammation-associated idiosyncratic drug hepatotoxicity. B. D. Cosgrove, B. M. King, M. A. Hasan, L. G. Alexopoulos, P. A. Farazi, B. S. Hendriks, L. G. Griffith, P. K. Sorger, B. Tidor, J. J. Xu, D. A. Lauffenburger. Toxicol. Appl. Pharmacol. 237: 319-330 (2009).
	CHARMM: The biomolecular simulation program. B. R. Brooks, C. L. Brooks III, A. D. Mackerell Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus. J. Comput. Chem. 30: 1545-1614 (2009).
	Sensitivity analysis for oscillating dynamical systems. A. K. Wilkins, B. Tidor, J. K. White, and P.I . Barton. SIAM J. Sci. Comput. 31: 2706-2732 (2009).
	A critical review on modelling formalisms and simulation tools in computational biosystems. D. Machado, R. S. Costa, M. Rocha, I. Rocha, B. Tidor, and E. C. Ferreira. Lecture Notes in Computer Science 5518: 1063-1070 (2009).
	Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements. M.D. Altman, J.P. Bardhan, J.K. White, and B. Tidor. J. Comput. Chem. 30: 132-153 (2009).
	Aglycosylated immunoglobulin G1 variants productively engage activating Fc receptors. S.L. Sazinsky, R.G. Ott, N.W. Silver, B. Tidor, J.V. Ravetch, K.D. Wittrup. Proc. Natl. Acad. Sci. U.S.A. 105: 20167-20172 (2008).
	Optimal drug cocktail design: Methods for targeting molecular ensembles and insights from theoretical model systems. M.L. Radhakrishnan and B. Tidor. J. Chem. Inf. Model. 48: 1055-1073 (2008).
	HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. M.D. Altman, A. Ali, G.S.K.K. Reddy, M.N.L. Nalam, S.G. Anjum, H. Cao, S. Chellappan, V. Kairys, M.X. Fernandes, M.K. Gilson, C.A. Schiffer, T.M. Rana, and B. Tidor. J. Am. Chem. Soc. 130: 6099-6113 (2008).
	Novel method for probing the specificity binding profile of ligands: Applications to HIV protease. W. Sherman and B. Tidor. Chem. Biol. Drug Des. 71: 387-407 (2008).
	Stimulus design for model selection and validation in cell signaling. J.F. Apgar, J.E. Toettcher, D. Endy, F.M. White, and B. Tidor. PLoS Comput. Biol. 4: e30 (2008).
	Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease. M. D. Altman, E. A. Nalivaika, M. Prabu-Jeyabalan, C. A. Schiffer, and B. Tidor. Proteins 70: 678-694 (2008).
	Computationally mapping sequence space to understand evolutionary protein engineering. K.A. Armstrong and B. Tidor. Biotechnol. Prog. 24: 62-73 (2008).
	The Per2 negative feedback loop sets the period in the mammalian circadian clock mechanism. A.K. Wilkins, P.I. Barton, and B. Tidor. PLoS Comput. Biol. 3: e242 (2007).
	Selection of horseradish peroxidase variants with enhanced enantioselectivity by yeast surface display. D. Lipovšek, E. Antipov, K.A. Armstrong, M.J. Olsen, A.M. Klibanov, B. Tidor, and K.D. Wittrup. Chem. Biol. 14: 1176-1185 (2007).
	Specificity in Molecular Design: A Physical Framework for Probing the Determinants of Binding Specificity and Promiscuity in a Biological Environment. M.L. Radhakrishnan and B. Tidor. J. Phys. Chem. B 111: 13419-13435 (2007).
	Computational design of antibody affinity improvement beyond in vivo maturation. S.M. Lippow, K.D. Wittrup, and B. Tidor. Nature Biotechnol. 25: 1171-1176 (2007).
	Progress in computational protein design. S. M. Lippow and B. Tidor. Curr. Opin. Biotechnol. 18: 305-311 (2007).
	A post-synaptic scaffold at the origin of the animal kingdom. O. Sakarya, K.A. Armstrong, M. Adamska, M. Adamski, I.-F. Wang, B. Tidor, B.M. Degnan, T.H. Oakley, and K.S. Kosik. PLoS One 2: e506 (2007).
	Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. S. Chellappan, G.S.K.K. Reddy, A. Ali, M.N.L. Nalam, S.G. Anjum, H. Cao , V. Kairys, M.X. Fernandes, M.D. Altman, B. Tidor, T. Rana, C. Schiffer, and M.K. Gilson. Chem. Biol. Drug Des. 69: 298-313 (2007).
	Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces. J. P. Bardhan, M. D. Altman, D. J. Willis, S. M. Lippow, B. Tidor, and J. K. White. J. Chem. Phys. 127: 014701 (2007).
	Biological network design strategies: discovery through dynamic optimization. B. S. Adiwijaya, P. I. Barton, and B. Tidor. Molecular Biosystems 2: 650-659 (2006).
	Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide. D. F. Green, A. T. Dennis, P. S. Fam, B. Tidor, and A. Jasanoff. Biochemistry 45: 12547-12559 (2006).
	Optimal charges in lead progression: A structure-based neuraminidase case study. K. A. Armstrong, B. Tidor, and A. C. Cheng. Journal of Medicinal Chemistry 49: 2470-2477 (2006).
	FFTSVD: A fast multiscale boundary-element method solver suitable for bio-MEMS and biomolecule simulation. M. D. Altman, J. P. Bardhan, B. Tidor, and J. K. White. IEEE Transactions on Computer-aided Design of Integrated Circuits and Systems 25: 274-284 (2006).
	An accurate surface formulation for biomolecule electrostatics in non-ionic solutions. M. D. Altman, J. P. Bardhan, J. K. White, and B. Tidor. IEEE Conference on Engineering in Medicine and Biology (2005).
	A curved panel integration technique for molecular surfaces. J. P. Bardhan, M. D. Altman, S. M. Lippow, B. Tidor, and J. K. White. International Conference on Modeling and Simulation of Microsystems (MSM) (2005).
	Quantitative methods for developing Fc mutants with extended half-lives. D. T. Kamei, B. J. Bao, M. S. Ricci, R. Deshpande, H. Xu, B. Tidor, and D. A. Lauffenburger. Biotechnology and Bioengineering 92: 748-760 (2005).
	Osmotic pressure of aqueous chondroitin sulfate solution: A molecular modeling investigation. M. Bathe, G. C. Rutledge, A. J. Grodzinsky, and B. Tidor. Biophysical Journal 89: 2357-2371 (2005).
	Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface. D. F. Green and B. Tidor. Proteins: Struct., Funct., Bioinf. 60: 644-657 (2005).
	Interdisciplinary research and education at the biology-engineering-computer science interface: a perspective. B. Tadmor and B. Tidor. Drug Discovery Today 10: 1183-1189 (2005).
	Defining Cdk5 ligand chemical space with small molecule inhibitors of Tau phosphorylation. J. S. Ahn, M. L. Radhakrishnan, M. Mapelli, S. Choi, B. Tidor, G. D. Cuny, A. Musacchio, L. A. Yeh, and K. S. Kosik. Chem. Biol. 12: 811-823 (2005).
	A coarse-grained molecular model for glycosaminoglycans: Application to chondroitin, chondroitin sulfate, and hyaluronic acid. M. Bathe, G. C. Rutledge, A. J. Grodzinsky, and B. Tidor. Biophys J. 88: 3870-3887 (2005).
	A computational method for the analysis and prediction of protein:phosphopeptide-binding sites. B. A. Joughin, B. Tidor, and M. B. Yaffe. Protein Sci. 14: 131-139 (2005).
	Action-at-a-distance interactions enhance protein binding affinity. B. A. Joughin, D. F. Green, and B. Tidor. Protein Sci. 14: 1363-1369 (2005).
	Biomolecule electrostatic optimization with an implicit Hessian. J. P. Bardhan, J. H. Lee, M. D. Altman, S. Leyffer, S. Benson, B. Tidor, and J. K. White. International Conference on Modeling and Simulation of Microsystems : (2004).
	X-ray structural and simulation analysis of a protein mutant: The value of a combined approach. C. Matos, J. D. Cohen, D. F. Green, B. Tidor, and M. Karplus. Proteins: Stuct., Funct., Bioinform. 55: 733-742 (2004).
	Optimal linearized Poisson-Boltzmann theory applied to the simulation of flexible polyelectrolytes in solution. M. Bathe, A. J. Grodzinsky, B. Tidor, and G. C. Rutledge. J. Chem. Phys. 121: 7557-7561 (2004).
	Escherichia coli glutaminyl-tRNA synthetase is electrostatically optimization for binding of its cognate substrates. D. F. Green and B. Tidor. J. Mol. Biol. 342: 435-452 (2004).
	Substantial energetic improvement with minimal structural perturbation in a high affinity mutant antibody. K. S. Midelfort, H. H. Hernandez, S. M. Lippow, B. Tidor, C. L. Drennan, and K. D. Wittrup. J. Mol. Biol. 343: 685-701 (2004).
	Computational and experimental probes of symmetry mismatches in the arc repressor-DNA complex. S. Spector, R. T. Sauer, and B. Tidor. J. Mol. Biol. 340: 253-261 (2004).
	Expression of N-formylated proteins in Escherichia coli.. S. Spector, J. M. Flynn, B. Tidor, T. A. Baker, and R. T. Sauer. Prot. Expr. Purif. 32: 317-322 (2003).
	Limitations of quantitative gene regulation models: A case study.. P. M. Kim and B. Tidor. Genome Res. 13: 2391-2395 (2003).
	Evaluation of ab initio charge determination methods for use in continuum solvation calculations.. D. F. Green and B. Tidor. J. Phys. Chem. B 107: 10261-10273 (2003).
	Coarse-graining glycosaminoglycans: Towards a multi-scale model of cartilage.. M. Bathe, G. C. Rutledge, A. J. Grodzinsky, and B. Tidor. 2nd Conference on Computational Fluid and Solid Mechanics : (2003).
	Fast methods for biomolecule charge optimization.. J. P. Bardhan, J. H. Lee, S. S. Kuo, M. D. Altman, B. Tidor, and J. K. White. Modeling and Simulation of Microsystems : (2003).
	Proteomic identification of 14-3-3 as a mitogen-activated protein kinase-activated protein kinase 2 substrate: Role in dimer formation and ligand binding.. D.W. Powell, M.J. Rane, B.A. Joughin, R. Kalmukova, J.H. Hong, B. Tidor, W. L. Dean, W. M. Pierce, J. B. Klein, M. B. Yaffe, and K. R. McLeish. Mol. Cell. Biol. 23: 5376-5387 (2003).
	Subsystem identification through dimensionality reduction of large-scale gene expression data.. P. M. Kim and B. Tidor. Genome Res. 13: 1706-1718 (2003).
	Surface salt bridges, double-mutant cycles, and protein stability: An experimental and computational analysis of the interaction of the Asp 23 side chain with the N-terminus of the N-terminal domain of the ribosomal protein L9.. D. L. Luisi, C. D. Snow, J. J. Lin, Z. S. Hendsch, B. Tidor, and D. P. Raleigh. Biochemistry 42: 7050-7060 (2003).
	Fast methods for simulation of biomolecule electrostatics.. S. S. Kuo, M. D. Altman, J. P. Bardhan, B. Tidor, and J. K. White. International Conference on Computer Aided Design : (2002).
	Rational Cytokine Design for Increased Lifetime and Enhanced Potency Using pH-activated "Histidine Switching.". C. A. Sarkar, K. Lowenhaupt, T. Horan, T. C. Boone, B. Tidor, and D. A. Lauffenburger. Nature Biotechnol. 20: 908-913 (2002).
	De Novo Determination of Peptide Structure with Solid-State Magic-Angle Spinning NMR Spectroscopy. C. M. Rienstra, L. Tucker-Kellogg, C. P. Jaroniec, M. Hohwy, B. Reif, M. T. McMahon, B. Tidor, T. Lozano-Pérez, and R. G. Griffin. Proc. Natl. Acad. Sci. U.S.A. 99: 10260-10265 (2002).
	Side-Chain Repacking Calculations for Predicting Structures and Stabilities of Heterodimeric Coiled Coils. A. E. Keating, V. N. Malashkevich, B. Tidor, and P. S. Kim. Proc. Natl. Acad. Sci. U.S.A. 98: 14825-14830 (2001).
	Barstar is Electrostatically Optimized for Tight-Binding to Barnase. L.-P. Lee and B. Tidor. Nature Struct. Biol. 8: 73-76 (2001).
	Electrostatic Complementarity at Ligand Binding Sites: Application to Chorismate Mutase. E. Kangas and B. Tidor. J. Phys. Chem. B 105: 880-888 (2001).
	Preferential Protein Heterodimer Formation via Introduction of Undercompensated Electrostatic Interactions. Z. S. Hendsch, M. J. Nohaile, R. T. Sauer, and B. Tidor. J. Am. Chem. Soc. 123: 1264-1265 (2001).
	Optimization of Binding Electrostatics: Charge Complementarity in the Barnase-Barstar Protein Complex. L.-P. Lee and B. Tidor. Protein Sci. 10: 362-377 (2001).
	Altering Dimerization Specificity by Changes in Surface Electrostatics. M. J. Nohaile, Z. S. Hendsch, B. Tidor, and R. T. Sauer. Proc. Natl. Acad. Sci. U.S.A. 98: 3109-3114 (2001).
	Electrostatic Specificity in Molecular Ligand Design. E. Kangas and B. Tidor. J. Chem. Phys. 112: 9120-9131 (2000).
	Rational Modification of Protein Stability by the Mutation of Charged Surface Residues. S. Spector, M. Wang, S. A. Carp, J. Robblee, Z. S. Hendsch, R. Fairman, B. Tidor and D. P. Raleigh. Biochemistry 39: 872-879 (2000).
	Electrostatic Optimization in Ligand Complimentarity Design. In: Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches (C. A. Floudas and P. M. Pardalos, eds.). E. Kangas and B. Tidor. Kluwer Academic Publishers, Boston pp.: 231-242 (2000).
	Electrostatic Interactions in theGCN4 Leucine Zipper: Effects of Intramolecular Interactions that are Enhanced on Binding. Z. S. Hendsch and B. Tidor. Protein Sci. 8: 1181-1192 (1999).
	Long-Range Electrostatic Contributions to Protein-Ligand Binding Estimated Using Protein Charge Ladders, Affinity Capillary Electrophoresis, and Continuum Electrostatics. J. A. Caravella, J. D. Carbeck, D. C. Duffy, G. M. Whitesides, and B. Tidor. J. Am. Chem. Soc. 121: 4340-4347 (1999).
	Charge Optimization Leads to Favorable Electrostatic Binding Free Energy.. E. Kangas and B. Tidor. Phys. Rev. E 59: 5958-5961 (1999).
	High-Resolution Protein Design with Backbone Freedom. P. B. Harbury, J. J. Plecs, B. Tidor, T. Alber and P. S. Kim. Science (Washington, D.C.) 282: 1462-1467 (1998).
	Optimizing Electrostatic Affinity in Ligand-Receptor Binding: Theory, Computation, and Ligand Properties.. E. Kangas and B. Tidor. J. Chem. Phys. 109: 7522-7545 (1998).
	Effects of Salt Bridges on Protein Structure and Design. C. V. Sindelar, Z. S. Hendsch, and B. Tidor. Protein Sci. 7: 1898-1914 (1998).
	AmbiPack: A Systematic Algorithm for Packing of Macromolecular Structures with Ambiguous Distance Constraints. C.-s. E. Wang, T. Lozano-Perez, and B. Tidor. Proteins: Struct., Funct., Genet. 32: 26-42 (1998).
	Parameter Dependence in Continuum Electrostatic Calculations. Z. S. Hendsch, C. V. Sindelar, and B. Tidor. J. Phys. Chem. B 102: 4404-4410 (1998).
	Computation of Electrostatic Complements to Proteins: A Case of Charge Stabilized Binding. L. T. Chong, S. E. Dempster, Z. S. Hendsch, L.-P. Lee, and B. Tidor. Protein Sci. 7: 206-210 (1998).
	Molecular-Modeling Calculations of Enzymatic Enantioselectivity Taking Hydration into Account. T. Ke, B. Tidor, and A. M. Klibanov. Biotechnology and Bioengineering 57: 741-745 (1998).
	Molecular Dynamics Simulations. B. Tidor. Current Biology 7: R525-R527 (1997).
	Computing Bounds on Free Energy Changes with One and Two Dimensional Paths. C. Jarque and B. Tidor. J. Phys. Chem. B 101: 9402-9409 (1997).
	Simulated Annealing on Coupled Free Energy Surfaces: Relative Solvation Energies of Small Molecules. C. Jarque and B. Tidor. J. Phys. Chem. B 101: 9362-9374 (1997).
	Optimization of Electrostatic Binding Free Energy. L.-P. Lee and B. Tidor. J. Chem. Phys. 106: 8681-8690 (1997).
	Protein Stabilization by Removal of Unsatisfied Polar Groups: Computational Approaches and Experimental Tests. Z. S. Hendsch, T. Jonsson, R. T. Sauer, and B. Tidor. Biochemistry 35: 7621-7625 (1996).
	Repacking Protein Cores with Backbone Freedom: Structure Prediction for Coiled Coils. P. B. Harbury, B. Tidor, and P. S. Kim. Proc. Natl. Acad. Sci. U.S.A. 92: 8404-8412 (1995).
	Helix-Capping Interaction in Lambda Cro Protein: A Free Energy Simulation Analysis. B. Tidor. Proteins: Struct., Funct., Genet. 19: 310-323 (1994).
	Do Salt Bridges Stabilize Proteins? A Continuum Electrostatic Analysis. Z. S. Hendsch and B. Tidor. Protein Sci. 3: 211-226 (1994).
	Simulated Annealing on Free Energy Surfaces by a Combined Molecular Dynamics and Monte Carlo Approach. B. Tidor. J. Phys. Chem. 97: 1069-1073 (1993).