Bruce Tidor - Publications

Affiliations: 
Biological Engineering Massachusetts Institute of Technology, Cambridge, MA, United States 
Area:
structure and properties of proteins, nucleic acids, and their complexes
Website:
http://web.mit.edu/be/people/tidor.shtml

180 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Zhao B, Sedlak JC, Srinivas R, Creixell P, Pritchard JR, Tidor B, Lauffenburger DA, Hemann MT. Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution. Cell. PMID 26924578 DOI: 10.1016/j.cell.2016.01.045  1
2015 Shen Y, Radhakrishnan ML, Tidor B. Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: lessons learned from HIV-1 protease inhibition. Proteins. 83: 351-72. PMID 25410041 DOI: 10.1002/prot.24730  0.96
2015 Hagen DR, Tidor B. Efficient Bayesian estimates for discrimination among topologically different systems biology models Molecular Biosystems. 11: 574-584. DOI: 10.1039/c4mb00276h  1
2015 Shen Y, Radhakrishnan ML, Tidor B. Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: Lessons learned from HIV-1 protease inhibition Proteins: Structure, Function and Bioinformatics. 83: 351-372. DOI: 10.1002/prot.24730  1
2014 Cui Y, Murphy B, Gentilcore A, Sharma Y, Minasian LM, Kramer BS, Coates PM, Gohagan JK, Klenk J, Tidor B. Multilevel modeling and value of information in clinical trial decision support. Bmc Systems Biology. 8: 6. PMID 25540094 DOI: 10.1186/s12918-014-0140-0  1
2013 Silver NW, King BM, Nalam MN, Cao H, Ali A, Kiran Kumar Reddy GS, Rana TM, Schiffer CA, Tidor B. Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration. Journal of Chemical Theory and Computation. 9: 5098-5115. PMID 24250277 DOI: 10.1021/ct400383v  1
2013 Nalam MN, Ali A, Reddy GS, Cao H, Anjum SG, Altman MD, Yilmaz NK, Tidor B, Rana TM, Schiffer CA. Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance. Chemistry & Biology. 20: 1116-24. PMID 24012370 DOI: 10.1016/j.chembiol.2013.07.014  1
2013 Shen Y, Altman MD, Ali A, Nalam MN, Cao H, Rana TM, Schiffer CA, Tidor B. Testing the substrate-envelope hypothesis with designed pairs of compounds. Acs Chemical Biology. 8: 2433-41. PMID 23952265 DOI: 10.1021/cb400468c  1
2013 Grácio F, Cabral J, Tidor B. Modeling Stem Cell Induction Processes Plos One. 8. PMID 23667423 DOI: 10.1371/journal.pone.0060240  1
2013 Toni T, Tidor B. Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology Plos Computational Biology. 9. PMID 23555205 DOI: 10.1371/journal.pcbi.1002960  1
2013 Hagen DR, White JK, Tidor B. Convergence in parameters and predictions using computational experimental design Interface Focus. 3. DOI: 10.1098/rsfs.2013.0008  1
2012 Shen Y, Gilson MK, Tidor B. Charge Optimization Theory for Induced-Fit Ligands. Journal of Chemical Theory and Computation. 8: 4580-4592. PMID 23162383 DOI: 10.1021/ct200931c  0.48
2012 Parai MK, Huggins DJ, Cao H, Nalam MN, Ali A, Schiffer CA, Tidor B, Rana TM. Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance. Journal of Medicinal Chemistry. 55: 6328-41. PMID 22708897 DOI: 10.1021/jm300238h  1
2012 Machado D, Costa RS, Ferreira EC, Rocha I, Tidor B. Exploring the gap between dynamic and constraint-based models of metabolism. Metabolic Engineering. 14: 112-9. PMID 22306209 DOI: 10.1016/j.ymben.2012.01.003  1
2012 Huggins DJ, Sherman W, Tidor B. Rational approaches to improving selectivity in drug design Journal of Medicinal Chemistry. 55: 1424-1444. PMID 22239221 DOI: 10.1021/jm2010332  1
2012 King BM, Silver NW, Tidor B. Efficient calculation of molecular configurational entropies using an information theoretic approximation Journal of Physical Chemistry B. 116: 2891-2904. DOI: 10.1021/jp2068123  1
2012 Shen Y, Gilson MK, Tidor B. Charge optimization theory for induced-fit ligands Journal of Chemical Theory and Computation. 8: 4580-4592. DOI: 10.1021/ct200931c  1
2011 Hagen DR, Apgar JF, Witmer DK, White FM, Tidor B. Reply to Comment on "Sloppy models, parameter uncertainty, and the role of experimental design" Molecular Biosystems. 7: 2523-2524. PMID 23148131 DOI: 10.1039/C1MB05200D  1
2011 Machado D, Costa RS, Rocha M, Ferreira EC, Tidor B, Rocha I. Modeling formalisms in Systems Biology. Amb Express. 1: 45. PMID 22141422 DOI: 10.1186/2191-0855-1-45  1
2011 Bahl N, Du R, Winarsih I, Ho B, Tucker-Kellogg L, Tidor B, Ding JL. Delineation of lipopolysaccharide (LPS)-binding sites on hemoglobin: From in silico predictions to biophysical characterization Journal of Biological Chemistry. 286: 37793-37803. PMID 21900232 DOI: 10.1074/jbc.M111.245472  1
2011 Huang L, Pan CQ, Li B, Tucker-Kellogg L, Tidor B, Chen Y, Low BC. Simulating EGFR-ERK signaling control by scaffold proteins KSR and MP1 reveals differential Ligand-Sensitivity Co-Regulated by CBL-CIN85 and Endophilin Plos One. 6. PMID 21829671 DOI: 10.1371/journal.pone.0022933  1
2011 Huggins DJ, Tidor B. Systematic placement of structural water molecules for improved scoring of protein-ligand interactions Protein Engineering, Design and Selection. 24: 777-789. PMID 21771870 DOI: 10.1093/protein/gzr036  1
2011 Wei XN, Han BC, Zhang JX, Liu XH, Tan CY, Jiang YY, Low BC, Tidor B, Chen YZ. An Integrated Mathematical Model of Thrombin-, Histamine-and VEGF-Mediated Signalling in Endothelial Permeability Bmc Systems Biology. 5. PMID 21756365 DOI: 10.1186/1752-0509-5-112  1
2011 Toettcher J, Castillo A, Tidor B, White J. Biochemical oscillator sensitivity analysis in the presence of conservation constraints Proceedings - Design Automation Conference. 806-811.  1
2010 Leonard E, Ajikumar PK, Thayer K, Xiao WH, Mo JD, Tidor B, Stephanopoulos G, Prather KLJ. Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control Proceedings of the National Academy of Sciences of the United States of America. 107: 13654-13659. PMID 20643967 DOI: 10.1073/pnas.1006138107  1
2010 Radhakrishnan ML, Tidor B. Cellular level models as tools for cytokine design Biotechnology Progress. 26: 919-937. PMID 20568274 DOI: 10.1002/btpr.387  1
2010 Apgar JF, Witmer DK, White FM, Tidor B. Sloppy models, parameter uncertainty, and the role of experimental design. Molecular Biosystems. 6: 1890-900. PMID 20556289 DOI: 10.1039/b918098b  1
2010 Nalam MN, Ali A, Altman MD, Reddy GS, Chellappan S, Kairys V, Ozen A, Cao H, Gilson MK, Tidor B, Rana TM, Schiffer CA. Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. Journal of Virology. 84: 5368-78. PMID 20237088 DOI: 10.1128/JVI.02531-09  0.44
2010 Machado D, Costa RS, Rocha M, Rocha I, Tidor B, Ferreira EC. Model transformation of metabolic networks using a Petri net based framework Ceur Workshop Proceedings. 827: 103-117.  1
2009 Bardhan JP, Altman MD, Tidor B, White JK. A "Reverse-Schur" Approach to Optimization With Linear PDE Constraints: Application to Biomolecule Analysis and Design. Journal of Chemical Theory and Computation. 5: 3260-3278. PMID 23055839  0.44
2009 Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, ... ... Tidor B, et al. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry. 30: 1545-614. PMID 19444816 DOI: 10.1002/jcc.21287  1
2009 Cosgrove BD, King BM, Hasan MA, Alexopoulos LG, Farazi PA, Hendriks BS, Griffith LG, Sorger PK, Tidor B, Xu JJ, Lauffenburger DA. Synergistic drug-cytokine induction of hepatocellular death as an in vitro approach for the study of inflammation-associated idiosyncratic drug hepatotoxicity. Toxicology and Applied Pharmacology. 237: 317-30. PMID 19362101 DOI: 10.1016/j.taap.2009.04.002  1
2009 King BM, Tidor B. MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets Bioinformatics. 25: 1165-1172. PMID 19261718 DOI: 10.1093/bioinformatics/btp109  1
2009 Jorissen RN, Reddy GS, Ali A, Altman MD, Chellappan S, Anjum SG, Tidor B, Schiffer CA, Rana TM, Gilson MK. Additivity in the analysis and design of HIV protease inhibitors. Journal of Medicinal Chemistry. 52: 737-54. PMID 19193159 DOI: 10.1021/jm8009525  0.44
2009 Zhang YL, Radhakrishnan ML, Lu X, Gross AW, Tidor B, Lodish HF. Symmetric signaling by an asymmetric 1 erythropoietin: 2 erythropoietin receptor complex. Molecular Cell. 33: 266-74. PMID 19187767 DOI: 10.1016/j.molcel.2008.11.026  1
2009 Toettcher JE, Loewer A, Ostheimer GJ, Yaffe MB, Tidor B, Lahav G. Distinct mechanisms act in concert to mediate cell cycle arrest Proceedings of the National Academy of Sciences of the United States of America. 106: 785-790. PMID 19139404 DOI: 10.1073/pnas.0806196106  1
2009 Hong EJ, Lippow SM, Tidor B, Lozano-Pérez T. Rotamer optimization for protein design through MAP estimation and problem-size reduction Journal of Computational Chemistry. 30: 1923-1945. PMID 19123203 DOI: 10.1002/jcc.21188  1
2009 Huggins DJ, Altman MD, Tidor B. Evaluation of an inverse molecular design algorithm in a model binding site Proteins: Structure, Function and Bioinformatics. 75: 168-186. PMID 18831031 DOI: 10.1002/prot.22226  1
2009 Altman MD, Bardhan JP, White JK, Tidor B. Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized poisson-boltzmann equation with curved boundary elements Journal of Computational Chemistry. 30: 132-153. PMID 18567005 DOI: 10.1002/jcc.21027  1
2009 Wilkins K, Tidor B, White J, Barton PI. Sensitivity analysis for oscilla ting dynamical systems Siam Journal On Scientific Computing. 31: 2706-2732. DOI: 10.1137/070707129  1
2009 Bardhan JP, Altman MD, Tidor B, White JK. "Reverse-schur" approach to optimization with linear pde constraints: Application to biomolecule analysis and design Journal of Chemical Theory and Computation. 5: 3260-3278. DOI: 10.1021/ct9001174  1
2009 Machado D, Costa RS, Rocha M, Rocha I, Tidor B, Ferreira EC. A critical review on modelling formalisms and simulation tools in computational biosystems Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5518: 1063-1070. DOI: 10.1007/978-3-642-02481-8_161  1
2008 Sazinsky SL, Ott RG, Silver NW, Tidor B, Ravetch JV, Wittrup KD. Aglycosylated immunoglobulin G1 variants productively engage activating Fc receptors. Proceedings of the National Academy of Sciences of the United States of America. 105: 20167-72. PMID 19074274 DOI: 10.1073/pnas.0809257105  1
2008 Radhakrishnan ML, Tidor B. Optimal drug cocktail design: methods for targeting molecular ensembles and insights from theoretical model systems. Journal of Chemical Information and Modeling. 48: 1055-73. PMID 18505239 DOI: 10.1021/ci700452r  0.96
2008 Altman MD, Ali A, Reddy GS, Nalam MN, Anjum SG, Cao H, Chellappan S, Kairys V, Fernandes MX, Gilson MK, Schiffer CA, Rana TM, Tidor B. HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. Journal of the American Chemical Society. 130: 6099-113. PMID 18412349 DOI: 10.1021/ja076558p  0.44
2008 Sherman W, Tidor B. Novel method for probing the specificity binding profile of ligands: Applications to HIV protease Chemical Biology and Drug Design. 71: 387-407. PMID 18384529 DOI: 10.1111/j.1747-0285.2008.00659.x  1
2008 Apgar JF, Toettcher JE, Endy D, White FM, Tidor B. Stimulus design for model selection and validation in cell signaling. Plos Computational Biology. 4: e30. PMID 18282085 DOI: 10.1371/journal.pcbi.0040030  1
2008 Armstrong KA, Tidor B. Computationally mapping sequence space to understand evolutionary protein engineering. Biotechnology Progress. 24: 62-73. PMID 18020358 DOI: 10.1021/bp070134h  1
2008 Altman MD, Nalivaika EA, Prabu-Jeyabalan M, Schiffer CA, Tidor B. Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease. Proteins. 70: 678-94. PMID 17729291 DOI: 10.1002/prot.21514  1
2008 Kuo SH, Tidor B, White J. A meshless, spectrally accurate, integral equation solver for molecular surface electrostatics Acm Journal On Emerging Technologies in Computing Systems. 4. DOI: 10.1145/1350763.1350766  1
2008 Radhakrishnan ML, Tidor B. Optimal drug cocktail design: Methods for targeting molecular ensembles and insights from theoretical model systems Journal of Chemical Information and Modeling. 48: 1055-1073. DOI: 10.1021/ci700452r  1
2007 Wilkins AK, Barton PI, Tidor B. The Per2 negative feedback loop sets the period in the mammalian circadian clock mechanism. Plos Computational Biology. 3: e242. PMID 18085817 DOI: 10.1371/journal.pcbi.0030242  1
2007 Radhakrishnan ML, Tidor B. Specificity in molecular design: a physical framework for probing the determinants of binding specificity and promiscuity in a biological environment. The Journal of Physical Chemistry. B. 111: 13419-35. PMID 17979267 DOI: 10.1021/jp074285e  0.96
2007 Lipovsek D, Antipov E, Armstrong KA, Olsen MJ, Klibanov AM, Tidor B, Wittrup KD. Selection of horseradish peroxidase variants with enhanced enantioselectivity by yeast surface display. Chemistry & Biology. 14: 1176-85. PMID 17961829 DOI: 10.1016/j.chembiol.2007.09.008  1
2007 Lipovsek D, Antipov E, Armstrong KA, Olsen MJ, Klibanov AM, Tidor B, Wittrup KD. Selection of horseradish peroxidase variants with enhanced enantioselectivity by yeast surface display. Chemistry & Biology. 14: 1176-85. PMID 17961829 DOI: 10.1016/j.chembiol.2007.09.008  1
2007 Lippow SM, Wittrup KD, Tidor B. Computational design of antibody-affinity improvement beyond in vivo maturation. Nature Biotechnology. 25: 1171-6. PMID 17891135 DOI: 10.1038/nbt1336  1
2007 Lippow SM, Wittrup KD, Tidor B. Computational design of antibody-affinity improvement beyond in vivo maturation. Nature Biotechnology. 25: 1171-6. PMID 17891135 DOI: 10.1038/nbt1336  1
2007 Lippow SM, Tidor B. Progress in computational protein design Current Opinion in Biotechnology. 18: 305-311. PMID 17644370 DOI: 10.1016/j.copbio.2007.04.009  1
2007 Bardhan JP, Altman MD, Willis DJ, Lippow SM, Tidor B, White JK. Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces Journal of Chemical Physics. 127. PMID 17627358 DOI: 10.1063/1.2743423  1
2007 Bardhan JP, Altman MD, Willis DJ, Lippow SM, Tidor B, White JK. Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces Journal of Chemical Physics. 127. PMID 17627358 DOI: 10.1063/1.2743423  0.52
2007 Sakarya O, Armstrong KA, Adamska M, Adamski M, Wang IF, Tidor B, Degnan BM, Oakley TH, Kosik KS. A post-synaptic scaffold at the origin of the animal kingdom. Plos One. 2: e506. PMID 17551586 DOI: 10.1371/journal.pone.0000506  1
2007 Sakarya O, Armstrong KA, Adamska M, Adamski M, Wang IF, Tidor B, Degnan BM, Oakley TH, Kosik KS. A post-synaptic scaffold at the origin of the animal kingdom. Plos One. 2: e506. PMID 17551586 DOI: 10.1371/journal.pone.0000506  1
2007 Chellappan S, Kiran Kumar Reddy GS, Ali A, Nalam MN, Anjum SG, Cao H, Kairys V, Fernandes MX, Altman MD, Tidor B, Rana TM, Schiffer CA, Gilson MK. Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chemical Biology & Drug Design. 69: 298-313. PMID 17539822 DOI: 10.1111/j.1747-0285.2007.00514.x  0.44
2007 Chellappan S, Kiran Kumar Reddy GS, Ali A, Nalam MNL, Anjum SG, Cao H, Kairys V, Fernandes MX, Altman MD, Tidor B, Rana TM, Schiffer CA, Gilson MK. Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis Chemical Biology and Drug Design. 69: 298-313. PMID 17539822 DOI: 10.1111/j.1747-0285.2007.00514.x  0.52
2007 Bardhan JP, Altman MD, White JK, Tidor B. Efficient optimization of electrostatic interactions between biomolecules Proceedings of the Ieee Conference On Decision and Control. 4563-4569. DOI: 10.1109/CDC.2007.4434808  1
2007 Bardhan JP, Altman MD, White JK, Tidor B. Efficient optimization of electrostatic interactions between biomolecules Proceedings of the Ieee Conference On Decision and Control. 4563-4569. DOI: 10.1109/CDC.2007.4434808  0.44
2007 Radhakrishnan ML, Tidor B. Specificity in molecular design: A physical framework for probing the determinants of binding specificity and promiscuity in a biological environment Journal of Physical Chemistry B. 111: 13419-13435. DOI: 10.1021/jp074285e  1
2007 Radhakrishnan ML, Tidor B. Specificity in molecular design: A physical framework for probing the determinants of binding specificity and promiscuity in a biological environment Journal of Physical Chemistry B. 111: 13419-13435. DOI: 10.1021/jp074285e  0.96
2006 Adiwijaya BS, Barton PI, Tidor B. Biological network design strategies: Discovery through dynamic optimization Molecular Biosystems. 2: 650-659. PMID 17216046 DOI: 10.1039/b610090b  1
2006 Green DF, Dennis AT, Fam PS, Tidor B, Jasanoff A. Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide. Biochemistry. 45: 12547-59. PMID 17029410 DOI: 10.1021/bi060857u  1
2006 Green DF, Dennis AT, Fam PS, Tidor B, Jasanoff A. Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide. Biochemistry. 45: 12547-59. PMID 17029410 DOI: 10.1021/bi060857u  1
2006 Armstrong KA, Tidor B, Cheng AC. Optimal charges in lead progression: a structure-based neuraminidase case study. Journal of Medicinal Chemistry. 49: 2470-7. PMID 16610790 DOI: 10.1021/jm051105l  1
2006 Armstrong KA, Tidor B, Cheng AC. Optimal charges in lead progression: a structure-based neuraminidase case study. Journal of Medicinal Chemistry. 49: 2470-7. PMID 16610790 DOI: 10.1021/jm051105l  1
2006 Altman MD, Bardhan JP, Tidor B, White JK. FFTSVD: A fast multiscale boundary-element method solver suitable for bio-MEMS and biomolecule simulation Ieee Transactions On Computer-Aided Design of Integrated Circuits and Systems. 25: 274-284. DOI: 10.1109/TCAD.2005.855946  1
2006 Altman MD, Bardhan JP, Tidor B, White JK. FFTSVD: A fast multiscale boundary-element method solver suitable for bio-MEMS and biomolecule simulation Ieee Transactions On Computer-Aided Design of Integrated Circuits and Systems. 25: 274-284. DOI: 10.1109/TCAD.2005.855946  0.44
2006 Altman MD, Bardhan JP, Tidor B, White JK. FFTSVD: A fast multiscale boundary element method solver suitable for Bio-MEMS and biomolecule simulation Design Automation Methods and Tools For Microfluidics-Based Biochips. 143-168. DOI: 10.1007/1-4020-5123-9_6  1
2006 Altman MD, Bardhan JP, Tidor B, White JK. FFTSVD: A fast multiscale boundary element method solver suitable for Bio-MEMS and biomolecule simulation Design Automation Methods and Tools For Microfluidics-Based Biochips. 143-168. DOI: 10.1007/1-4020-5123-9_6  0.44
2005 Tadmor B, Tidor B. Interdisciplinary research and education at the biology-engineering- computer science interface: A perspective Drug Discovery Today. 10: 1183-1189. PMID 16182211 DOI: 10.1016/S1359-6446(05)03540-3  1
2005 Kamei DT, Lao BJ, Ricci MS, Deshpande R, Xu H, Tidor B, Lauffenburger DA. Quantitative methods for developing Fc mutants with extended half-lives Biotechnology and Bioengineering. 92: 748-760. PMID 16136591 DOI: 10.1002/bit.20624  1
2005 Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. Osmotic pressure of aqueous chondroitin sulfate solution: a molecular modeling investigation. Biophysical Journal. 89: 2357-71. PMID 16055525 DOI: 10.1529/biophysj.105.067918  1
2005 Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. Osmotic pressure of aqueous chondroitin sulfate solution: a molecular modeling investigation. Biophysical Journal. 89: 2357-71. PMID 16055525 DOI: 10.1529/biophysj.105.067918  1
2005 Ahn JS, Radhakrishnan ML, Mapelli M, Choi S, Tidor B, Cuny GD, Musacchio A, Yeh LA, Kosik KS. Defining Cdk5 ligand chemical space with small molecule inhibitors of tau phosphorylation. Chemistry & Biology. 12: 811-23. PMID 16039528 DOI: 10.1016/j.chembiol.2005.05.011  1
2005 Ahn JS, Radhakrishnan ML, Mapelli M, Choi S, Tidor B, Cuny GD, Musacchio A, Yeh LA, Kosik KS. Defining Cdk5 ligand chemical space with small molecule inhibitors of tau phosphorylation. Chemistry & Biology. 12: 811-23. PMID 16039528 DOI: 10.1016/j.chembiol.2005.05.011  1
2005 Green DF, Tidor B. Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface. Proteins. 60: 644-57. PMID 16001428 DOI: 10.1002/prot.20540  1
2005 Green DF, Tidor B. Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface. Proteins. 60: 644-57. PMID 16001428 DOI: 10.1002/prot.20540  1
2005 Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. A coarse-grained molecular model for glycosaminoglycans: application to chondroitin, chondroitin sulfate, and hyaluronic acid. Biophysical Journal. 88: 3870-87. PMID 15805173 DOI: 10.1529/biophysj.104.058800  1
2005 Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. A coarse-grained molecular model for glycosaminoglycans: application to chondroitin, chondroitin sulfate, and hyaluronic acid. Biophysical Journal. 88: 3870-87. PMID 15805173 DOI: 10.1529/biophysj.104.058800  1
2005 Joughin BA, Green DF, Tidor B. Action-at-a-distance interactions enhance protein binding affinity. Protein Science : a Publication of the Protein Society. 14: 1363-9. PMID 15802650 DOI: 10.1110/ps.041283105  1
2005 Joughin BA, Green DF, Tidor B. Action-at-a-distance interactions enhance protein binding affinity. Protein Science : a Publication of the Protein Society. 14: 1363-9. PMID 15802650 DOI: 10.1110/ps.041283105  1
2005 Joughin BA, Tidor B, Yaffe MB. A computational method for the analysis and prediction of protein: Phosphopeptide-binding sites Protein Science. 14: 131-139. PMID 15576564 DOI: 10.1110/ps.04964705  1
2005 Joughin BA, Tidor B, Yaffe MB. A computational method for the analysis and prediction of protein: Phosphopeptide-binding sites Protein Science. 14: 131-139. PMID 15576564 DOI: 10.1110/ps.04964705  0.52
2005 Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. Effects of chemical composition on chondroitin sulfate osmotic pressure and aggrecan conformation Proceedings of the 2005 Summer Bioengineering Conference. 2005: 667-668.  1
2005 Wilkins AK, Tidor B, Barton PI. Boundary value formulation for the sensitivity analysis of biological oscillators with application to the circadian oscillator Aiche Annual Meeting, Conference Proceedings. 6777-6778.  1
2005 Wilkins AK, Tidor B, Barton PI. Boundary value formulation for the sensitivity analysis of biological oscillators with application to the circadian oscillator Aiche Annual Meeting, Conference Proceedings. 6777-6778.  0.16
2005 Altman MD, Bardhan JP, White JK, Tidor B. An accurate surface formulation for biomolecule electrostatics in non-ionic solutions Annual International Conference of the Ieee Engineering in Medicine and Biology - Proceedings. 7: 7591-7595.  1
2005 Altman MD, Bardhan JP, White JK, Tidor B. An accurate surface formulation for biomolecule electrostatics in non-ionic solutions Annual International Conference of the Ieee Engineering in Medicine and Biology - Proceedings. 7: 7591-7595.  0.44
2005 Bardhan JP, Altman MD, Lippow SM, Tidor B, White JK. A curved panel integration technique for molecular surfaces 2005 Nsti Nanotechnology Conference and Trade Show - Nsti Nanotech 2005 Technical Proceedings. 512-515.  1
2005 Bardhan JP, Altman MD, Lippow SM, Tidor B, White JK. A curved panel integration technique for molecular surfaces 2005 Nsti Nanotechnology Conference and Trade Show - Nsti Nanotech 2005 Technical Proceedings. 512-515.  0.44
2005 Adiwijaya B, Barton PI, Tidor B. Biological network design principles: Discovery through optimization Aiche Annual Meeting, Conference Proceedings. 11695.  1
2005 Lippow SM, Tidor B, Wittrup KD. Antibody affinity maturation using computational protein design Aiche Annual Meeting, Conference Proceedings. 10505.  1
2005 Lippow SM, Tidor B, Wittrup KD. Antibody affinity maturation using computational protein design Aiche Annual Meeting, Conference Proceedings. 10505.  0.44
2004 Bathe M, Grodzinsky AJ, Tidor B, Rutledge GC. Optimal linearized Poisson-Boltzmann theory applied to the simulation of flexible polyelectrolytes in solution. The Journal of Chemical Physics. 121: 7557-61. PMID 15485214 DOI: 10.1063/1.1808411  1
2004 Bathe M, Grodzinsky AJ, Tidor B, Rutledge GC. Optimal linearized Poisson-Boltzmann theory applied to the simulation of flexible polyelectrolytes in solution. The Journal of Chemical Physics. 121: 7557-61. PMID 15485214 DOI: 10.1063/1.1808411  1
2004 Midelfort KS, Hernandez HH, Lippow SM, Tidor B, Drennan CL, Wittrup KD. Substantial energetic improvement with minimal structural perturbation in a high affinity mutant antibody. Journal of Molecular Biology. 343: 685-701. PMID 15465055 DOI: 10.1016/j.jmb.2004.08.019  1
2004 Midelfort KS, Hernandez HH, Lippow SM, Tidor B, Drennan CL, Wittrup KD. Substantial energetic improvement with minimal structural perturbation in a high affinity mutant antibody. Journal of Molecular Biology. 343: 685-701. PMID 15465055 DOI: 10.1016/j.jmb.2004.08.019  1
2004 Green DF, Tidor B. Escherichia coli glutaminyl-tRNA synthetase is electrostatically optimized for binding of its cognate substrates. Journal of Molecular Biology. 342: 435-52. PMID 15327945 DOI: 10.1016/j.jmb.2004.06.087  1
2004 Green DF, Tidor B. Escherichia coli glutaminyl-tRNA synthetase is electrostatically optimized for binding of its cognate substrates. Journal of Molecular Biology. 342: 435-52. PMID 15327945 DOI: 10.1016/j.jmb.2004.06.087  1
2004 Spector S, Sauer RT, Tidor B. Computational and experimental probes of symmetry mismatches in the Arc repressor-DNA complex. Journal of Molecular Biology. 340: 253-61. PMID 15201050 DOI: 10.1016/j.jmb.2004.04.026  1
2004 Spector S, Sauer RT, Tidor B. Computational and experimental probes of symmetry mismatches in the Arc repressor-DNA complex. Journal of Molecular Biology. 340: 253-61. PMID 15201050 DOI: 10.1016/j.jmb.2004.04.026  1
2004 Mattos C, Cohen JD, Green DF, Tidor B, Karplus M. X-ray structural and simulation analysis of a protein mutant: the value of a combined approach. Proteins. 55: 733-42. PMID 15103635 DOI: 10.1002/prot.20031  1
2004 Mattos C, Cohen JD, Green DF, Tidor B, Karplus M. X-ray structural and simulation analysis of a protein mutant: the value of a combined approach. Proteins. 55: 733-42. PMID 15103635 DOI: 10.1002/prot.20031  1
2004 Bardhan JP, Lee JH, Altman MD, Leyffer S, Benson S, Tidor B, White JK. Biomolecule electrostatic optimization with an implicit hessian 2004 Nsti Nanotechnology Conference and Trade Show - Nsti Nanotech 2004. 1: 164-167.  1
2004 Bardhan JP, Lee JH, Altman MD, Leyffer S, Benson S, Tidor B, White JK. Biomolecule electrostatic optimization with an implicit hessian 2004 Nsti Nanotechnology Conference and Trade Show - Nsti Nanotech 2004. 1: 164-167.  0.44
2003 Green DF, Tidor B. Evaluation of electrostatic interactions. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 8.3. PMID 18428710 DOI: 10.1002/0471250953.bi0803s02  1
2003 Green DF, Tidor B. Evaluation of electrostatic interactions. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 8.3. PMID 18428710 DOI: 10.1002/0471250953.bi0803s02  1
2003 Spector S, Flynn JM, Tidor B, Baker TA, Sauer RT. Expression of N-formylated proteins in Escherichia coli. Protein Expression and Purification. 32: 317-22. PMID 14965779 DOI: 10.1016/j.pep.2003.08.004  1
2003 Spector S, Flynn JM, Tidor B, Baker TA, Sauer RT. Expression of N-formylated proteins in Escherichia coli. Protein Expression and Purification. 32: 317-22. PMID 14965779 DOI: 10.1016/j.pep.2003.08.004  1
2003 Kim PM, Tidor B. Limitations of quantitative gene regulation models: A case study Genome Research. 13: 2391-2395. PMID 14597653 DOI: 10.1101/gr.1207003  1
2003 Powell DW, Rane MJ, Joughin BA, Kalmukova R, Hong JH, Tidor B, Dean WL, Pierce WM, Klein JB, Yaffe MB, McLeish KR. Proteomic identification of 14-3-3ζ as a mitogen-activated protein kinase-activated protein kinase 2 substrate: Role in dimer formation and ligand binding Molecular and Cellular Biology. 23: 5376-5387. PMID 12861023 DOI: 10.1128/MCB.23.15.5376-5387.2003  1
2003 Powell DW, Rane MJ, Joughin BA, Kalmukova R, Hong JH, Tidor B, Dean WL, Pierce WM, Klein JB, Yaffe MB, McLeish KR. Proteomic identification of 14-3-3ζ as a mitogen-activated protein kinase-activated protein kinase 2 substrate: Role in dimer formation and ligand binding Molecular and Cellular Biology. 23: 5376-5387. PMID 12861023 DOI: 10.1128/MCB.23.15.5376-5387.2003  0.52
2003 Kim PM, Tidor B. Subsystem identification through dimensionality reduction of large-scale gene expression data Genome Research. 13: 1706-1718. PMID 12840046 DOI: 10.1101/gr.903503  1
2003 Luisi DL, Snow CD, Lin JJ, Hendsch ZS, Tidor B, Raleigh DP. 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 Biochemistry. 42: 7050-7060. PMID 12795600 DOI: 10.1021/bi027202n  1
2003 Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. Towards a multi-scale model of cartilage: Coarse-graining glycosaminoglycans Computational Fluid and Solid Mechanics 2003. 1626-1630. DOI: 10.1016/B978-008044046-0.50396-1  1
2003 Bardhan JP, Lee JH, Kuo SS, Altman MD, Tidor B, White JK. Fast methods for biomolecule charge optimization 2003 Nanotechnology Conference and Trade Show - Nanotech 2003. 2: 508-511.  1
2003 Bardhan JP, Lee JH, Kuo SS, Altman MD, Tidor B, White JK. Fast methods for biomolecule charge optimization 2003 Nanotechnology Conference and Trade Show - Nanotech 2003. 2: 508-511.  0.44
2003 Green DF, Tidor B. Evaluation of ab initio charge determination methods for use in continuum solvation calculations Journal of Physical Chemistry B. 107: 10261-10273.  1
2003 Green DF, Tidor B. Evaluation of ab initio charge determination methods for use in continuum solvation calculations Journal of Physical Chemistry B. 107: 10261-10273.  0.96
2002 Sarkar CA, Lowenhaupt K, Horan T, Boone TC, Tidor B, Lauffenburger DA. Rational cytokine design for increased lifetime and enhanced potency using pH-activated "histidine switching" Nature Biotechnology. 20: 908-913. PMID 12161759 DOI: 10.1038/nbt725  1
2002 Rienstra CM, Tucker-Kellogg L, Jaroniec CP, Hohwy M, Reif B, McMahon MT, Tidor B, Lozano-Pérez T, Griffin RG. De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 99: 10260-5. PMID 12149447 DOI: 10.1073/pnas.152346599  1
2002 Rienstra CM, Tucker-Kellogg L, Jaroniec CP, Hohwy M, Reif B, McMahon MT, Tidor B, Lozano-Pérez T, Griffin RG. De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 99: 10260-5. PMID 12149447 DOI: 10.1073/pnas.152346599  1
2002 Kuo SS, Altman MD, Bardhan JP, Tidor B, White JK. Fast methods for simulation of biomolecule electrostatics Ieee/Acm International Conference On Computer-Aided Design, Digest of Technical Papers. 466-470. DOI: 10.1145/774572.774640  1
2002 Kuo SS, Altman MD, Bardhan JP, Tidor B, White JK. Fast methods for simulation of biomolecule electrostatics Ieee/Acm International Conference On Computer-Aided Design, Digest of Technical Papers. 466-470. DOI: 10.1145/774572.774640  0.44
2002 Kamei DT, Tidor B, Lauffenburger DA. Design of Fc-conjugated protein therapeutics using computational modeling of protein-protein interaction energetics Annual International Conference of the Ieee Engineering in Medicine and Biology - Proceedings. 1: 616.  1
2001 Keating AE, Malashkevich VN, Tidor B, Kim PS. Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils. Proceedings of the National Academy of Sciences of the United States of America. 98: 14825-30. PMID 11752430 DOI: 10.1073/pnas.261563398  1
2001 Keating AE, Malashkevich VN, Tidor B, Kim PS. Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils. Proceedings of the National Academy of Sciences of the United States of America. 98: 14825-30. PMID 11752430 DOI: 10.1073/pnas.261563398  1
2001 Hendsch ZS, Nohaile MJ, Sauer RT, Tidor B. Preferential heterodimer formation via undercompensated electrostatic interactions [18] Journal of the American Chemical Society. 123: 1264-1265. PMID 11456695 DOI: 10.1021/ja0032273  1
2001 Lee LP, Tidor B. Optimization of binding electrostatics: Charge complementarity in the barnase-barstar protein complex Protein Science. 10: 362-377. PMID 11266622 DOI: 10.1110/ps.40001  1
2001 Nohaile MJ, Hendsch ZS, Tidor B, Sauer RT. Altering dimerization specificity by changes in surface electrostatics Proceedings of the National Academy of Sciences of the United States of America. 98: 3109-3114. PMID 11248040 DOI: 10.1073/pnas.051624498  1
2001 Lee LP, Tidor B. Barstar is electrostatically optimized for tight binding to barnase Nature Structural Biology. 8: 73-76. PMID 11135675 DOI: 10.1038/83082  1
2001 Kangast E, Tidor B. Electrostatic complementarity at ligand binding sites: Application to chorismate mutase Journal of Physical Chemistry B. 105: 880-888.  1
2000 Spector S, Wang M, Carp SA, Robblee J, Hendsch ZS, Fairman R, Tidor B, Raleigh DP. Rational modification of protein stability by the mutation of charged surface residues. Biochemistry. 39: 872-9. PMID 10653630 DOI: 10.1021/bi992091m  1
2000 Kangas E, Tidor B. Electrostatic specificity in molecular ligand design Journal of Chemical Physics. 112: 9120-9131.  1
2000 Kangas E, Tidor B. Electrostatic specificity in molecular ligand design Journal of Chemical Physics. 112: 9120-9131.  1
1999 Kangas E, Tidor B. Charge optimization leads to favorable electrostatic binding free energy. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 59: 5958-61. PMID 11969577  1
1999 Hendsch ZS, Tidor B. Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding. Protein Science : a Publication of the Protein Society. 8: 1381-92. PMID 10422826 DOI: 10.1110/ps.8.7.1381  1
1999 Caravell JA, Carbeck JD, Duffy DC, Whitesides GM, Tidor B. Long-range electrostatic contributions to protein-ligand binding estimated using protein charge ladders, affinity capillary electrophoresis, and continuum electrostatic theory Journal of the American Chemical Society. 121: 4340-4347. DOI: 10.1021/ja984195a  1
1998 Ke T, Tidor B, Klibanov AM. Molecular-modeling calculations of enzymatic enantioselectivity taking hydration into account. Biotechnology and Bioengineering. 57: 741-5. PMID 10099253 DOI: 10.1002/(SICI)1097-0290(19980320)57:6<741::AID-BIT11>3.0.CO;2-A  1
1998 Harbury PB, Plecs JJ, Tidor B, Alber T, Kim PS. High-resolution protein design with backbone freedom. Science (New York, N.Y.). 282: 1462-7. PMID 9822371  1
1998 Sindelar CV, Hendsch ZS, Tidor B. Effects of salt bridges on protein structure and design. Protein Science : a Publication of the Protein Society. 7: 1898-914. PMID 9761471 DOI: 10.1002/pro.5560070906  1
1998 Wang CS, Lozano-Pérez T, Tidor B. AmbiPack: a systematic algorithm for packing of macromolecular structures with ambiguous distance constraints. Proteins. 32: 26-42. PMID 9672040 DOI: 10.1002/(SICI)1097-0134(19980701)32:1<26::AID-PROT5>3.0.CO;2-C  1
1998 Chong LT, Dempster SE, Hendsch ZS, Lee LP, Tidor B. Computation of electrostatic complements to proteins: a case of charge stabilized binding. Protein Science : a Publication of the Protein Society. 7: 206-10. PMID 9514276 DOI: 10.1002/pro.5560070122  1
1998 Kangas E, Tidor B. Optimizing electrostatic affinity in ligand-receptor binding: Theory, computation, and ligand properties Journal of Chemical Physics. 109: 7522-7545. DOI: 10.1063/1.477375  1
1998 Hendsch ZS, Sindelar CV, Tidor B. Parameter dependence in continuum electrostatic calculations: A study using protein salt bridges Journal of Physical Chemistry B. 102: 4404-4410.  1
1997 Tidor B. Molecular dynamics simulations. Current Biology : Cb. 7: R525-7. PMID 9285726  1
1997 Jarque C, Tidor B. Computing bounds on free energy changes with one and two dimensional paths Journal of Physical Chemistry B. 101: 9402-9409.  1
1997 Jarque C, Tidor B. Simulated annealing on coupled free energy surfaces: Relative solvation energies of small molecules Journal of Physical Chemistry B. 101: 9362-9374.  1
1997 Lee LP, Tidor B. Optimization of electrostatic binding free energy Journal of Chemical Physics. 106: 8681-8690.  1
1996 Hendsch ZS, Jonsson T, Sauer RT, Tidor B. Protein stabilization by removal of unsatisfied polar groups: computational approaches and experimental tests. Biochemistry. 35: 7621-5. PMID 8672461 DOI: 10.1021/bi9605191  1
1995 Harbury PB, Tidor B, Kim PS. Repacking protein cores with backbone freedom: structure prediction for coiled coils. Proceedings of the National Academy of Sciences of the United States of America. 92: 8408-12. PMID 7667303 DOI: 10.1073/pnas.92.18.8408  1
1995 Lansbury PT, Costa PR, Griffiths JM, Simon EJ, Auger M, Halverson KJ, Kocisko DA, Hendsch ZS, Ashburn TT, Spencer RG. Structural model for the beta-amyloid fibril based on interstrand alignment of an antiparallel-sheet comprising a C-terminal peptide. Nature Structural Biology. 2: 990-8. PMID 7583673  1
1994 Tidor B, Karplus M. The contribution of vibrational entropy to molecular association. The dimerization of insulin. Journal of Molecular Biology. 238: 405-14. PMID 8176732 DOI: 10.1006/jmbi.1994.1300  1
1994 Hendsch ZS, Tidor B. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Science : a Publication of the Protein Society. 3: 211-26. PMID 8003958 DOI: 10.1002/pro.5560030206  1
1994 Tidor B. Helix-capping interaction in lambda Cro protein: a free energy simulation analysis. Proteins. 19: 310-23. PMID 7984627 DOI: 10.1002/prot.340190406  1
1993 Hu JC, Newell NE, Tidor B, Sauer RT. Probing the roles of residues at the e and g positions of the GCN4 leucine zipper by combinatorial mutagenesis. Protein Science : a Publication of the Protein Society. 2: 1072-84. PMID 8102921 DOI: 10.1002/pro.5560020701  1
1993 Tidor B, Karplus M. The contribution of cross-links to protein stability: a normal mode analysis of the configurational entropy of the native state. Proteins. 15: 71-9. PMID 7680808 DOI: 10.1002/prot.340150109  1
1993 Tidor B. Simulated annealing on free energy surfaces by a combined molecular dynamics and Monte Carlo approach Journal of Physical Chemistry. 97: 1069-1073.  1
1991 Tidor B, Karplus M. Simulation analysis of the stability mutant R96H of T4 lysozyme. Biochemistry. 30: 3217-28. PMID 2009262  1
1991 Prevost M, Wodak SJ, Tidor B, Karplus M. Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase. Proceedings of the National Academy of Sciences of the United States of America. 88: 10880-4. PMID 1961758  1
1991 Karplus M, Prévost M, Tidor B, Wodak S. Simulation analysis of the stability mutants R96H of bacteriophage T4 lysozyme and I96A of barnase. Ciba Foundation Symposium. 161: 63-74. PMID 1814697  1
1991 Calnan BJ, Tidor B, Biancalana S, Hudson D, Frankel AD. Arginine-mediated RNA recognition: the arginine fork. Science (New York, N.Y.). 252: 1167-71. PMID 1709522  1
1991 Ha S, Gao J, Tidor B, Brady JW, Karplus M. Solvent effect on the anomeric equilibrium in D-glucose: A free energy simulation analysis Journal of the American Chemical Society. 113: 1553-1557.  1
1990 Kuczera K, Gao J, Tidor B, Karplus M. Free energy of sickling: A simulation analysis. Proceedings of the National Academy of Sciences of the United States of America. 87: 8481-5. PMID 2236057  1
1990 Smith J, Cusack S, Tidor B, Karplus M. Inelastic neutron scattering analysis of low-frequency motions in proteins: Harmonic and damped harmonic models of bovine pancreatic tryspin inhibitor The Journal of Chemical Physics. 93: 2974-2991.  1
1989 Gao J, Kuczera K, Tidor B, Karplus M. Hidden thermodynamics of mutant proteins: a molecular dynamics analysis. Science (New York, N.Y.). 244: 1069-72. PMID 2727695  1
1989 Smith J, Kuczera K, Tidor B, Doster W, Cusack S, Karplus M. Internal dynamics of globular proteins: Comparison of neutron scattering measurements and theoretical models Physica B: Physics of Condensed Matter. 156: 437-443. DOI: 10.1016/0921-4526(89)90699-6  1
1988 Cusack S, Smith J, Finney J, Tidor B, Karplus M. Inelastic neutron scattering analysis of picosecond internal protein dynamics. Comparison of harmonic theory with experiment. Journal of Molecular Biology. 202: 903-8. PMID 2459399 DOI: 10.1016/0022-2836(88)90566-9  1
1985 Irikura KK, Tidor B, Brooks BR, Karplus M. Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference. Science (New York, N.Y.). 229: 571-2. PMID 3839596  1
1983 Tidor B, Irikura KK, Brooks BR, Karplus M. Dynamics of DNA oligomers. Journal of Biomolecular Structure & Dynamics. 1: 231-52. PMID 6400872 DOI: 10.1080/07391102.1983.10507437  1
1983 Von Ragué Schleyer P, Tidor B, Jemmis ED, Chandrasekhar J, Würthwein EU, Kos AJ, Luke BT, Pople JA. Lithium-stabilized methanonium ions, CLi5-nHn +. A theoretical study Journal of the American Chemical Society. 105: 484-488.  1
1982 Pople JA, Tidor B, Schleyer PvR. The structure and stability of dications derived from methane Chemical Physics Letters. 88: 533-537. DOI: 10.1016/0009-2614(82)85003-3  1
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