| Year |
Citation |
Score |
| 2016 |
Traxlmayr MW, Kiefer JD, Srinivas RR, Lobner E, Tisdale AW, Mehta NK, Yang NJ, Tidor B, Wittrup KD. Strong Enrichment of Aromatic Residues in Binding Sites from a Charge-Neutralized Hyperthermostable Sso7d Scaffold Library. The Journal of Biological Chemistry. PMID 27582495 DOI: 10.1074/Jbc.M116.741314 |
0.368 |
|
| 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 |
0.725 |
|
| 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 |
0.638 |
|
| 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 |
0.573 |
|
| 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 |
0.51 |
|
| 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 |
0.537 |
|
| 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 |
0.385 |
|
| 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 |
0.708 |
|
| 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 |
0.615 |
|
| 2012 |
King BM, Silver NW, Tidor B. Efficient calculation of molecular configurational entropies using an information theoretic approximation. The Journal of Physical Chemistry. B. 116: 2891-904. PMID 22229789 DOI: 10.1021/Jp2068123 |
0.363 |
|
| 2012 |
Bahl N, Tidor B, Ding JL. LPS-Binding Sites On the Hemoglobin Tetramer - Prediction and Validation Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.385 |
0.343 |
|
| 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 |
0.673 |
|
| 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 |
0.655 |
|
| 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 |
0.665 |
|
| 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 |
0.668 |
|
| 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 |
0.689 |
|
| 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 |
0.539 |
|
| 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 DOI: 10.1021/Ct9001174 |
0.331 |
|
| 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 |
0.738 |
|
| 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 |
0.536 |
|
| 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 |
0.659 |
|
| 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 |
0.462 |
|
| 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 |
0.653 |
|
| 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 |
0.674 |
|
| 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 |
0.334 |
|
| 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 |
0.691 |
|
| 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 |
0.552 |
|
| 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 |
0.369 |
|
| 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 |
0.319 |
|
| 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 |
0.565 |
|
| 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 |
0.655 |
|
| 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 |
0.723 |
|
| 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 |
0.357 |
|
| 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 |
0.519 |
|
| 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 |
0.67 |
|
| 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 |
0.527 |
|
| 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 |
0.527 |
|
| 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 |
0.359 |
|
| 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 |
0.71 |
|
| 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 |
0.71 |
|
| 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 |
0.657 |
|
| 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 |
0.657 |
|
| 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 |
0.547 |
|
| 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 |
0.547 |
|
| 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 |
0.72 |
|
| 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 |
0.72 |
|
| 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 |
0.745 |
|
| 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 |
0.745 |
|
| 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 |
0.744 |
|
| 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. |
0.62 |
|
| 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 |
0.707 |
|
| 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 |
0.707 |
|
| 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 |
0.54 |
|
| 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 |
0.54 |
|
| 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 |
0.476 |
|
| 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 |
0.476 |
|
| 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 |
0.712 |
|
| 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 |
0.712 |
|
| 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 |
0.519 |
|
| 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 |
0.519 |
|
| 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 |
0.426 |
|
| 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 |
0.426 |
|
| 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 |
0.729 |
|
| 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 |
0.354 |
|
| 2003 |
Rienstra C, Griffin R, Lozano-Perez T, Tidor B, McMahon M, Reif B, Hohwy M, Tucker-Kellogg L, Jaroniec C. 13C and 15N Chemical Shift Assignments for f-MLF-OH Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr5934 |
0.613 |
|
| 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. DOI: 10.1021/Jp0350971 |
0.534 |
|
| 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 |
0.669 |
|
| 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 |
0.355 |
|
| 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 |
0.745 |
|
| 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 |
0.745 |
|
| 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 |
0.729 |
|
| 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 |
0.729 |
|
| 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 |
0.478 |
|
| 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 |
0.413 |
|
| 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 |
0.498 |
|
| 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 |
0.385 |
|
| 2001 |
Kangast E, Tidor B. Electrostatic complementarity at ligand binding sites: Application to chorismate mutase Journal of Physical Chemistry B. 105: 880-888. DOI: 10.1021/Jp003449N |
0.357 |
|
| 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 |
0.362 |
|
| 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 DOI: 10.1103/Physreve.59.5958 |
0.366 |
|
| 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 |
0.402 |
|
| 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 |
0.396 |
|
| 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 |
0.331 |
|
| 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 DOI: 10.1126/Science.282.5393.1462 |
0.509 |
|
| 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 |
0.347 |
|
| 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 |
0.629 |
|
| 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 |
0.678 |
|
| 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 |
0.367 |
|
| 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. DOI: 10.1021/Jp9728666 |
0.332 |
|
| 1997 |
Tidor B. Molecular dynamics simulations. Current Biology : Cb. 7: R525-7. PMID 9285726 DOI: 10.1016/S0960-9822(06)00269-7 |
0.316 |
|
| 1997 |
Lee LP, Tidor B. Optimization of electrostatic binding free energy Journal of Chemical Physics. 106: 8681-8690. DOI: 10.1063/1.473929 |
0.344 |
|
| 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. DOI: 10.1021/Jp9716795 |
0.313 |
|
| 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. DOI: 10.1021/Jp9640181 |
0.348 |
|
| 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 |
0.541 |
|
| 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 |
0.501 |
|
| 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 |
0.479 |
|
| 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 |
0.389 |
|
| 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 |
0.359 |
|
| 1994 |
Nardi F, Doster W, Tidor B, Karplus M, Cusack S, Smith J. Dynamics of tRNA: Experimental Neutron Spectra Compared with a Normal Mode Analysis Israel Journal of Chemistry. 34: 233-238. DOI: 10.1002/Ijch.199400026 |
0.534 |
|
| 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 |
0.519 |
|
| 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 |
0.453 |
|
| 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. DOI: 10.1021/J100107A015 |
0.313 |
|
| 1991 |
Tidor B, Karplus M. Simulation analysis of the stability mutant R96H of T4 lysozyme. Biochemistry. 30: 3217-28. PMID 2009262 DOI: 10.1021/Bi00227A009 |
0.503 |
|
| 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 DOI: 10.1073/Pnas.88.23.10880 |
0.496 |
|
| 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 DOI: 10.1002/9780470514146.ch5 |
0.416 |
|
| 1991 |
Prévost M, Wodak S, Tidor B, Karplus M. Contribution of the hydrophobic effect to protein stability : molecular dynamics simulations of the lie → Ala mutation in Barnase Journal De Chimie Physique. 88: 2727-2728. DOI: 10.1051/Jcp/1991882727 |
0.467 |
|
| 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. DOI: 10.1021/Ja00005A015 |
0.6 |
|
| 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 DOI: 10.1073/Pnas.87.21.8481 |
0.629 |
|
| 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. DOI: 10.1063/1.458885 |
0.523 |
|
| 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 DOI: 10.1126/Science.2727695 |
0.628 |
|
| 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 |
0.548 |
|
| 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 |
0.558 |
|
| 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 DOI: 10.1126/Science.3839596 |
0.549 |
|
| 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 |
0.585 |
|
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