Bruce Tidor

发表

An Integrated Mathematical Model of Thrombin-, Histamine-and VEGF-Mediated Signalling in Endothelial Permeability

XiaoNa Wei, Bu-Cong Han, Jing-Xian Zhang, 2011, BMC Systems Biology.

Development of dynamic multi-layered bioprocess models

Bruce Tidor, Pedro Evangelista, Miguel Rocha, 2012 .

Sloppy models, parameter uncertainty, and the role of experimental design.

Bruce Tidor, Joshua F Apgar, David K Witmer, 2010, Molecular bioSystems.

Convergence in parameters and predictions using computational experimental design

Jacob K. White, Bruce Tidor, David R. Hagen, 2013, Interface Focus.

Modeling formalisms in Systems Biology

Miguel Rocha, Isabel Rocha, Rafael S. Costa, 2011, AMB Express.

Accurate solution of multi‐region continuum biomolecule electrostatic problems using the linearized Poisson–Boltzmann equation with curved boundary elements

Jacob K. White, Jaydeep P. Bardhan, Bruce Tidor, 2009, J. Comput. Chem..

Efficient Bayesian estimates for discrimination among topologically different systems biology models.

Bruce Tidor, David R Hagen, B. Tidor, 2014, Molecular bioSystems.

Biochemical oscillator sensitivity analysis in the presence of conservation constraints

Jacob K. White, Bruce Tidor, Anya Castillo, 2011, 2011 48th ACM/EDAC/IEEE Design Automation Conference (DAC).

Recycling Circuit Simulation Techniques for Mass-Action Biochemical Kinetics

Jacob K. White, Bruce Tidor, Jared E. Toettcher, 2011 .

CHARMM: The biomolecular simulation program

Jianpeng Ma, Charles L. Brooks, Themis Lazaridis, 2009, J. Comput. Chem..

The Per2 Negative Feedback Loop Sets the Period in the Mammalian Circadian Clock Mechanism

Paul I. Barton, Bruce Tidor, A. Katharina Wilkins, 2007, PLoS Comput. Biol..

Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology

Bruce Tidor, Tina Toni, B. Tidor, 2013, PLoS Comput. Biol..

Fast methods for simulation of biomolecule electrostatics

Jacob K. White, Jaydeep P. Bardhan, Bruce Tidor, 2002, ICCAD 2002.

Multilevel modeling and value of information in clinical trial decision support

Bruce Tidor, Brendan Murphy, Paul M Coates, 2014, BMC Systems Biology.

Progress in computational protein design.

Bruce Tidor, Shaun M Lippow, B. Tidor, 2007, Current opinion in biotechnology.

A meshless, spectrally accurate, integral equation solver for molecular surface electrostatics

Jacob K. White, Bruce Tidor, Shih-Hsien Kuo, 2008, JETC.

Interdisciplinary research and education at the biology-engineering-computer science interface: a perspective (reprinted article)

Bruce Tidor, Brigitta Tadmor, 2005 .

Optimal Drug Cocktail Design: Methods for Targeting Molecular Ensembles and Insights from Theoretical Model Systems

Bruce Tidor, Mala L. Radhakrishnan, B. Tidor, 2008, J. Chem. Inf. Model..

Stimulus Design for Model Selection and Validation in Cell Signaling

Drew Endy, Forest M. White, Bruce Tidor, 2008, PLoS Comput. Biol..

Sensitivity Analysis for Oscillating Dynamical Systems

Jacob K. White, Paul I. Barton, Bruce Tidor, 2009, SIAM J. Sci. Comput..

A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2009, IWANN.

Fast methods for simulation of biomolecule electrostatics

Jacob K. White, Jaydeep P. Bardhan, Bruce Tidor, 2002, IEEE/ACM International Conference on Computer Aided Design, 2002. ICCAD 2002..

Interdisciplinary research and education at the biology-engineering-computer science interface: a perspective.

Bruce Tidor, Brigitta Tadmor, 2005, Drug discovery today.

MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets

Bruce Tidor, Bracken M. King, B. Tidor, 2009, Bioinform..

Rotamer optimization for protein design through MAP estimation and problem‐size reduction

Tomás Lozano-Pérez, Bruce Tidor, Shaun M. Lippow, 2009, J. Comput. Chem..

Biological network design strategies: discovery through dynamic optimization.

Bruce Tidor, P. I. Barton, Bambang S Adiwijaya, 2006, Molecular bioSystems.

numerical Techniques in Biomolecule Design and Systems Biology

Jaydeep P. Bardhan, Paul I. Barton, Bruce Tidor, 2005 .

Efficient optimization of electrostatic interactions between biomolecules

Jacob K. White, Jaydeep P. Bardhan, Bruce Tidor, 2007, 2007 46th IEEE Conference on Decision and Control.

Model Transformation of Metabolic Networks using a Petri Net Based Framework

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2010, ACSD/Petri Nets Workshops.

Biomolecule Electrostatic Optimization with an Implicit Hessian

Jaydeep P. Bardhan, Bruce Tidor, Jacob White, 2004 .

Exploring the gap between dynamic and constraint-based models of metabolism.

Isabel Rocha, Bruce Tidor, Daniel Machado, 2012, Metabolic engineering.

Reply to Comment on "Sloppy models, parameter uncertainty, and the role of experimental design"

Bruce Tidor, Joshua F Apgar, David K Witmer, 2011, Molecular bioSystems.

Increased Flexibility in Genetic Algorithms: the Use of variable Boltzmann Selective pressure to control Propagation

Bruce Tidor, Michael de la Maza, B. Tidor, 1992, Computer Science and Operations Research.

Boltzmannn Weighted Selection Improves Performance of Genetic Algorithms

Bruce Tidor, Michael de la Maza, 1991 .

FFTSVD: A Fast Multiscale Boundary-Element Method Solver Suitable for Bio-MEMS and Biomolecule Simulation

Jacob K. White, Jaydeep P. Bardhan, Bruce Tidor, 2006, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems.

An Analysis of Selection Procedures with Particular Attention Paid to Proportional and Boltzmann Selection

Bruce Tidor, Michael de la Maza, B. Tidor, 1993, International Conference on Genetic Algorithms.

A computational method for the analysis and prediction of protein:phosphopeptide‐binding sites

Bruce Tidor, Michael B Yaffe, Brian A Joughin, 2005, Protein science : a publication of the Protein Society.

Additivity in the analysis and design of HIV protease inhibitors.

Bruce Tidor, Michael K Gilson, Akbar Ali, 2009, Journal of medicinal chemistry.

Defining Cdk5 ligand chemical space with small molecule inhibitors of tau phosphorylation.

Andrea Musacchio, Bruce Tidor, Mala L Radhakrishnan, 2005, Chemistry & biology.

Probing the roles of residues at the e and g positions of the GCN4 leucine zipper by combinatorial mutagenesis

James C. Hu, Bruce Tidor, B. Tidor, 1993, Protein science : a publication of the Protein Society.

Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces.

Jacob K. White, Bruce Tidor, Jaydeep P Bardhan, 2007, The Journal of chemical physics.

Aglycosylated immunoglobulin G1 variants productively engage activating Fc receptors

Bruce Tidor, Stephen L. Sazinsky, B. Tidor, 2008, Proceedings of the National Academy of Sciences.

Evaluation of an inverse molecular design algorithm in a model binding site

Bruce Tidor, David J Huggins, Michael D Altman, 2009, Proteins.

Structural model for the β-amyloid fibril based on interstrand alignment of an antiparallel-sheet comprising a C-terminal peptide

Eric J. Simon, Bruce Tidor, Peter T. Lansbury, 1995, Nature Structural Biology.

Design of improved protein inhibitors of HIV‐1 cell entry: Optimization of electrostatic interactions at the binding interface

Bruce Tidor, B. Tidor, D. F. Green, 2005, Proteins.

Long-Range Electrostatic Contributions to Protein-Ligand Binding Estimated Using Protein Charge Ladders, Affinity Capillary Electrophoresis, and Continuum Electrostatic Theory

George M. Whitesides, Bruce Tidor, David C. Duffy, 1999 .

A coarse-grained molecular model for glycosaminoglycans: application to chondroitin, chondroitin sulfate, and hyaluronic acid.

Mark Bathe, Bruce Tidor, Gregory C Rutledge, 2005, Biophysical journal.

Specificity in molecular design: a physical framework for probing the determinants of binding specificity and promiscuity in a biological environment.

Bruce Tidor, Mala L Radhakrishnan, Mala L. Radhakrishnan, 2007, The journal of physical chemistry. B.

Electrostatic interactions in the GCN4 leucine zipper: Substantial contributions arise from intramolecular interactions enhanced on binding

Bruce Tidor, B. Tidor, Z. Hendsch, 1999, Protein science : a publication of the Protein Society.

Inelastic neutron scattering analysis of low-frequency motions in proteins : harmonic and damped harmonic models of bovine pancreatic tryspin inhibitor

Bruce Tidor, Martin Karplus, Jeremy C. Smith, 1990 .

Testing the Substrate-Envelope Hypothesis with Designed Pairs of Compounds

Hong Cao, Bruce Tidor, Celia A. Schiffer, 2013, ACS chemical biology.

Limitations of quantitative gene regulation models: a case study.

Bruce Tidor, Philip M. Kim, Philip M Kim, 2003, Genome research.

Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis

Bruce Tidor, Brian M. Bonk, Brian M Bonk, 2019, Journal of the American Chemical Society.

Design of Mutation‐resistant HIV Protease Inhibitors with the Substrate Envelope Hypothesis

Hong Cao, Bruce Tidor, Michael K Gilson, 2007, Chemical biology & drug design.

Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance.

Hong Cao, Bruce Tidor, Nese Kurt Yilmaz, 2013, Chemistry & biology.

Electrostatic Optimization in Ligand Complementarity and Design

Bruce Tidor, B. Tidor, Erik Kangas, 2000 .

Barstar is electrostatically optimized for tight binding to barnase

Bruce Tidor, B. Tidor, L. Lee, 2001, Nature Structural Biology.

Electrostatic Complementarity at Ligand Binding Sites: Application to Chorismate Mutase

Bruce Tidor, B. Tidor, and Erik Kangas, 2001 .

Simulated annealing on free energy surfaces by a combined molecular dynamics and Monte Carlo approach

Bruce Tidor, B. Tidor, 1993 .

Computationally Mapping Sequence Space To Understand Evolutionary Protein Engineering

Bruce Tidor, B. Tidor, Kathryn A Armstrong, 2008, Biotechnology progress.

Proteomic Identification of 14-3-3ζ as a Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 Substrate: Role in Dimer Formation and Ligand Binding

Bruce Tidor, Michael B. Yaffe, David W. Powell, 2003, Molecular and Cellular Biology.

Efficient calculation of molecular configurational entropies using an information theoretic approximation.

Bruce Tidor, Bracken M. King, B. Tidor, 2012, The journal of physical chemistry. B.

Optimization of binding electrostatics: Charge complementarity in the barnase‐barstar protein complex

Bruce Tidor, B. Tidor, L. Lee, 2001, Protein science : a publication of the Protein Society.

Optimization of electrostatic binding free energy

Bruce Tidor, B. Tidor, L. Lee, 1997 .

Simulated Annealing on Coupled Free Energy Surfaces: Relative Solvation Energies of Small Molecules

Bruce Tidor, Cristina Jarque, 1997 .

Solvent effect on the anomeric equilibrium in D-glucose: a free energy simulation analysis

Bruce Tidor, Jiali Gao, Martin Karplus, 1991 .

Quantitative methods for developing Fc mutants with extended half-lives.

Bruce Tidor, Daniel T Kamei, Douglas A Lauffenburger, 2005, Biotechnology and bioengineering.

Action‐at‐a‐distance interactions enhance protein binding affinity

Bruce Tidor, Brian A Joughin, Brian A. Joughin, 2005, Protein science : a publication of the Protein Society.

Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: Lessons learned from HIV‐1 protease inhibition

Bruce Tidor, Mala L Radhakrishnan, Mala L. Radhakrishnan, 2015, Proteins.

HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants.

Hong Cao, Bruce Tidor, Michael K Gilson, 2008, Journal of the American Chemical Society.

Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide.

Bruce Tidor, Alan Jasanoff, B. Tidor, 2006, Biochemistry.

PARAMETER DEPENDENCE IN CONTINUUM ELECTROSTATIC CALCULATIONS : A STUDY USING PROTEIN SALT BRIDGES

Bruce Tidor, Zachary S. Hendsch, Charles V. Sindelar, 1998 .

A Curved Panel Integration Technique for Molecular Surfaces

Jacob K. White, Jaydeep P. Bardhan, Bruce Tidor, 2005 .

Electrostatic specificity in molecular ligand design

Bruce Tidor, B. Tidor, Erik Kangas, 2000 .

Computational design of antibody-affinity improvement beyond in vivo maturation

Bruce Tidor, Shaun M Lippow, B. Tidor, 2007, Nature Biotechnology.

Optimal charges in lead progression: a structure-based neuraminidase case study.

Bruce Tidor, Alan C Cheng, B. Tidor, 2006, Journal of medicinal chemistry.

Optimizing electrostatic affinity in ligand-receptor binding: Theory, computation, and ligand properties

Bruce Tidor, B. Tidor, Erik Kangas, 1998 .

Distinct mechanisms act in concert to mediate cell cycle arrest

Bruce Tidor, Michael B Yaffe, Jared E Toettcher, 2009, Proceedings of the National Academy of Sciences.

Evaluating the Substrate-Envelope Hypothesis: Structural Analysis of Novel HIV-1 Protease Inhibitors Designed To Be Robust against Drug Resistance

Michael K. Gilson, Hong Cao, Bruce Tidor, 2010, Journal of Virology.

Simulating EGFR-ERK Signaling Control by Scaffold Proteins KSR and MP1 Reveals Differential Ligand-Sensitivity Co-Regulated by Cbl-CIN85 and Endophilin

Lisa Tucker-Kellogg, Boon Chuan Low, Bruce Tidor, 2011, PloS one.

Systematic placement of structural water molecules for improved scoring of protein-ligand interactions.

Bruce Tidor, David J Huggins, B. Tidor, 2011, Protein engineering, design & selection : PEDS.