List of works - B Tidor

A "Reverse-Schur" Approach to Optimization With Linear PDE Constraints: Application to Biomolecule Analysis and Design

scientific article

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

scientific article

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

scientific article

A post-synaptic scaffold at the origin of the animal kingdom

scientific article published on 6 June 2007

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

scientific article

Action-at-a-distance interactions enhance protein binding affinity.

scientific article published on 31 March 2005

Aglycosylated immunoglobulin G1 variants productively engage activating Fc receptors

scholarly article

An accurate surface formulation for biomolecule electrostatics in non-ionic solutions.

scientific article published in January 2005

Arginine-mediated RNA recognition: the arginine fork.

scientific article

Barstar is electrostatically optimized for tight binding to barnase

scientific article published on 01 January 2001

Biological network design strategies: discovery through dynamic optimization.

scientific article published on 27 October 2006

Charge Optimization Theory for Induced-Fit Ligands.

scientific article published on 17 June 2012

Charge optimization leads to favorable electrostatic binding free energy

scientific article published on 01 May 1999

Combined model of intrinsic and extrinsic variability for computational network design with application to synthetic biology

scientific article

Computational and experimental probes of symmetry mismatches in the Arc repressor-DNA complex.

scientific article

Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease

scientific article

Computational design of antibody-affinity improvement beyond in vivo maturation

scientific article

Computationally mapping sequence space to understand evolutionary protein engineering.

scientific article

Convergence in parameters and predictions using computational experimental design.

scientific article published on August 2013

De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy.

scientific article

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

scientific article published in July 2005

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

scientific article published in September 2005

Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis

scientific article

Design, Synthesis, and Biological and Structural Evaluations of Novel HIV-1 Protease Inhibitors To Combat Drug Resistance

scientific article

Distinct mechanisms act in concert to mediate cell cycle arrest

scholarly article

Do salt bridges stabilize proteins? A continuum electrostatic analysis.

scientific article

Dynamics of DNA oligomers

scientific article published on 01 October 1983

Effects of salt bridges on protein structure and design.

scientific article

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

scientific article published in February 2015

Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration

scientific article

Efficient calculation of molecular configurational entropies using an information theoretic approximation

scientific article

Entropy of Two-Molecule Correlated Translational-Rotational Motions Using the <i>k</i>th Nearest Neighbor Method

scientific article published on 16 April 2021

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

scientific article

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

scientific article

Evaluation of electrostatic interactions.

scientific article published in August 2003

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

scientific article published on 28 January 2012

Expression of N-formylated proteins in Escherichia coli.

scientific article

HIV-1 Protease Inhibitors from Inverse Design in the Substrate Envelope Exhibit Subnanomolar Binding to Drug-Resistant Variants

scientific article

Helix-capping interaction in lambda Cro protein: a free energy simulation analysis.

scientific article published in August 1994

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis

scientific article published on 01 June 1989

High-resolution protein design with backbone freedom

scientific article

Inelastic neutron scattering analysis of picosecond internal protein dynamics

article

Intramolecular Hydrogen Bonding Restricts Gd-Aqua-Ligand Dynamics.

scientific article

Limitations of quantitative gene regulation models: a case study.

scientific article

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

scientific article

Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis

scientific article published on 21 February 2019

Modeling stem cell induction processes.

scientific article

Molecular dynamics simulations

scientific article published on 01 September 1997

Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: lessons learned from HIV-1 protease inhibition.

scientific article published on February 2015

Molecular-modeling calculations of enzymatic enantioselectivity taking hydration into account

scientific article published on 01 March 1998

Multilevel modeling and value of information in clinical trial decision support.

scientific article

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

scientific article

Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex.

scientific article published on February 2001

Osmotic pressure of aqueous chondroitin sulfate solution: a molecular modeling investigation.

scientific article

Preferential heterodimer formation via undercompensated electrostatic interactions.

scientific article published in February 2001

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

scientific article

Protein stabilization by removal of unsatisfied polar groups: computational approaches and experimental tests

scientific article published on 01 June 1996

Proteomic identification of 14-3-3zeta as a mitogen-activated protein kinase-activated protein kinase 2 substrate: role in dimer formation and ligand binding

scientific article

Rational Modification of Protein Stability by the Mutation of Charged Surface Residues†

scientific article published on 01 February 2000

Rational approaches to improving selectivity in drug design

scientific article

Rational cytokine design for increased lifetime and enhanced potency using pH-activated "histidine switching".

scientific article published on 5 August 2002

Rational design of thiolase substrate specificity for metabolic engineering applications

scientific article published on 29 June 2018

Repacking protein cores with backbone freedom: structure prediction for coiled coils

scientific article

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

scientific article published on August 2011

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

scientific article

SENSITIVITY ANALYSIS FOR OSCILLATING DYNAMICAL SYSTEMS.

scientific article published on June 2009

Selection of horseradish peroxidase variants with enhanced enantioselectivity by yeast surface display.

scientific article

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

scientific article published on 3 November 2007

Stimulus design for model selection and validation in cell signaling

scientific article

Strong Enrichment of Aromatic Residues in Binding Sites from a Charge-neutralized Hyperthermostable Sso7d Scaffold Library.

scientific article

Subsystem identification through dimensionality reduction of large-scale gene expression data

scientific article

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.

scientific article published on June 2003

Synergistic drug-cytokine induction of hepatocellular death as an in vitro approach for the study of inflammation-associated idiosyncratic drug hepatotoxicity.

scientific article

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

scientific article

Testing the substrate-envelope hypothesis with designed pairs of compounds.

scientific article published on 26 September 2013

The contribution of cross‐links to protein stability: A normal mode analysis of the configurational entropy of the native state ⬇️

scientific article published on January 1, 1993

The contribution of vibrational entropy to molecular association. The dimerization of insulin.

scientific article published in May 1994

Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference

scientific article

X-ray structural and simulation analysis of a protein mutant: the value of a combined approach.

scientific article published in May 2004

List of works by B Tidor

A "Reverse-Schur" Approach to Optimization With Linear PDE Constraints: Application to Biomolecule Analysis and Design

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

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

A post-synaptic scaffold at the origin of the animal kingdom

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

Action-at-a-distance interactions enhance protein binding affinity.

Aglycosylated immunoglobulin G1 variants productively engage activating Fc receptors

An accurate surface formulation for biomolecule electrostatics in non-ionic solutions.

Arginine-mediated RNA recognition: the arginine fork.

Barstar is electrostatically optimized for tight binding to barnase

Biological network design strategies: discovery through dynamic optimization.

Charge Optimization Theory for Induced-Fit Ligands.

Charge optimization leads to favorable electrostatic binding free energy

Combined model of intrinsic and extrinsic variability for computational network design with application to synthetic biology

Computational and experimental probes of symmetry mismatches in the Arc repressor-DNA complex.

Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease

Computational design of antibody-affinity improvement beyond in vivo maturation

Computationally mapping sequence space to understand evolutionary protein engineering.

Convergence in parameters and predictions using computational experimental design.

De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy.

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

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

Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis

Design, Synthesis, and Biological and Structural Evaluations of Novel HIV-1 Protease Inhibitors To Combat Drug Resistance

Distinct mechanisms act in concert to mediate cell cycle arrest

Do salt bridges stabilize proteins? A continuum electrostatic analysis.

Dynamics of DNA oligomers

Effects of salt bridges on protein structure and design.

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

Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration

Efficient calculation of molecular configurational entropies using an information theoretic approximation

Entropy of Two-Molecule Correlated Translational-Rotational Motions Using the <i>k</i>th Nearest Neighbor Method

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

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

Evaluation of electrostatic interactions.

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

Expression of N-formylated proteins in Escherichia coli.

HIV-1 Protease Inhibitors from Inverse Design in the Substrate Envelope Exhibit Subnanomolar Binding to Drug-Resistant Variants

Helix-capping interaction in lambda Cro protein: a free energy simulation analysis.

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis

High-resolution protein design with backbone freedom

Inelastic neutron scattering analysis of picosecond internal protein dynamics

Intramolecular Hydrogen Bonding Restricts Gd-Aqua-Ligand Dynamics.

Limitations of quantitative gene regulation models: a case study.

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

Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis

Modeling stem cell induction processes.

Molecular dynamics simulations

Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: lessons learned from HIV-1 protease inhibition.

Molecular-modeling calculations of enzymatic enantioselectivity taking hydration into account

Multilevel modeling and value of information in clinical trial decision support.

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

Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex.

Osmotic pressure of aqueous chondroitin sulfate solution: a molecular modeling investigation.

Preferential heterodimer formation via undercompensated electrostatic interactions.

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

Protein stabilization by removal of unsatisfied polar groups: computational approaches and experimental tests

Proteomic identification of 14-3-3zeta as a mitogen-activated protein kinase-activated protein kinase 2 substrate: role in dimer formation and ligand binding

Rational Modification of Protein Stability by the Mutation of Charged Surface Residues†

Rational approaches to improving selectivity in drug design

Rational cytokine design for increased lifetime and enhanced potency using pH-activated "histidine switching".

Rational design of thiolase substrate specificity for metabolic engineering applications

Repacking protein cores with backbone freedom: structure prediction for coiled coils

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

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

SENSITIVITY ANALYSIS FOR OSCILLATING DYNAMICAL SYSTEMS.

Selection of horseradish peroxidase variants with enhanced enantioselectivity by yeast surface display.

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

Stimulus design for model selection and validation in cell signaling

Strong Enrichment of Aromatic Residues in Binding Sites from a Charge-neutralized Hyperthermostable Sso7d Scaffold Library.

Subsystem identification through dimensionality reduction of large-scale gene expression data

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.

Synergistic drug-cytokine induction of hepatocellular death as an in vitro approach for the study of inflammation-associated idiosyncratic drug hepatotoxicity.

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

Testing the substrate-envelope hypothesis with designed pairs of compounds.

The contribution of cross‐links to protein stability: A normal mode analysis of the configurational entropy of the native state ⬇️

The contribution of vibrational entropy to molecular association. The dimerization of insulin.

Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference

X-ray structural and simulation analysis of a protein mutant: the value of a combined approach.