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Items: 1 to 50 of 110

1.

Rational design of thiolase substrate specificity for metabolic engineering applications.

Bonk BM, Tarasova Y, Hicks MA, Tidor B, Prather KLJ.

Biotechnol Bioeng. 2018 Jun 7. doi: 10.1002/bit.26737. [Epub ahead of print]

PMID:
29877597
2.

Intramolecular Hydrogen Bonding Restricts Gd-Aqua-Ligand Dynamics.

Boros E, Srinivas R, Kim HK, Raitsimring AM, Astashkin AV, Poluektov OG, Niklas J, Horning AD, Tidor B, Caravan P.

Angew Chem Int Ed Engl. 2017 May 8;56(20):5603-5606. doi: 10.1002/anie.201702274. Epub 2017 Apr 11.

3.

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

Traxlmayr MW, Kiefer JD, Srinivas RR, Lobner E, Tisdale AW, Mehta NK, Yang NJ, Tidor B, Wittrup KD.

J Biol Chem. 2016 Oct 21;291(43):22496-22508. Epub 2016 Aug 30.

4.

A Fungal-Selective Cytochrome bc1 Inhibitor Impairs Virulence and Prevents the Evolution of Drug Resistance.

Vincent BM, Langlois JB, Srinivas R, Lancaster AK, Scherz-Shouval R, Whitesell L, Tidor B, Buchwald SL, Lindquist S.

Cell Chem Biol. 2016 Aug 18;23(8):978-991. doi: 10.1016/j.chembiol.2016.06.016. Epub 2016 Aug 11.

5.

Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution.

Zhao B, Sedlak JC, Srinivas R, Creixell P, Pritchard JR, Tidor B, Lauffenburger DA, Hemann MT.

Cell. 2016 Mar 24;165(1):234-246. doi: 10.1016/j.cell.2016.01.045. Epub 2016 Feb 25.

6.

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

Cui Y, Murphy B, Gentilcore A, Sharma Y, Minasian LM, Kramer BS, Coates PM, Gohagan JK, Klenk J, Tidor B.

BMC Syst Biol. 2014 Dec 24;8:6. doi: 10.1186/s12918-014-0140-0.

7.

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

Hagen DR, Tidor B.

Mol Biosyst. 2015 Feb;11(2):574-84. doi: 10.1039/c4mb00276h.

PMID:
25460000
9.

Convergence in parameters and predictions using computational experimental design.

Hagen DR, White JK, Tidor B.

Interface Focus. 2013 Aug 6;3(4):20130008. doi: 10.1098/rsfs.2013.0008.

10.

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

Silver NW, King BM, Nalam MN, Cao H, Ali A, Kiran Kumar Reddy GS, Rana TM, Schiffer CA, Tidor B.

J Chem Theory Comput. 2013 Nov 12;9(11):5098-5115. Epub 2013 Aug 7.

11.

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

Nalam MN, Ali A, Reddy GS, Cao H, Anjum SG, Altman MD, Yilmaz NK, Tidor B, Rana TM, Schiffer CA.

Chem Biol. 2013 Sep 19;20(9):1116-24. doi: 10.1016/j.chembiol.2013.07.014. Epub 2013 Sep 5.

12.

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

Shen Y, Altman MD, Ali A, Nalam MN, Cao H, Rana TM, Schiffer CA, Tidor B.

ACS Chem Biol. 2013 Nov 15;8(11):2433-41. doi: 10.1021/cb400468c. Epub 2013 Sep 26.

13.

Modeling stem cell induction processes.

Grácio F, Cabral J, Tidor B.

PLoS One. 2013 May 8;8(5):e60240. doi: 10.1371/journal.pone.0060240. Print 2013.

14.

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

Toni T, Tidor B.

PLoS Comput Biol. 2013;9(3):e1002960. doi: 10.1371/journal.pcbi.1002960. Epub 2013 Mar 28.

15.

Charge Optimization Theory for Induced-Fit Ligands.

Shen Y, Gilson MK, Tidor B.

J Chem Theory Comput. 2012 Nov 13;8(11):4580-4592. Epub 2012 Jun 17.

16.

Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance.

Parai MK, Huggins DJ, Cao H, Nalam MN, Ali A, Schiffer CA, Tidor B, Rana TM.

J Med Chem. 2012 Jul 26;55(14):6328-41. doi: 10.1021/jm300238h. Epub 2012 Jul 13.

17.

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

Machado D, Costa RS, Ferreira EC, Rocha I, Tidor B.

Metab Eng. 2012 Mar;14(2):112-9. doi: 10.1016/j.ymben.2012.01.003. Epub 2012 Jan 28.

18.

Rational approaches to improving selectivity in drug design.

Huggins DJ, Sherman W, Tidor B.

J Med Chem. 2012 Feb 23;55(4):1424-44. doi: 10.1021/jm2010332. Epub 2012 Jan 12. Review. No abstract available.

19.

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

King BM, Silver NW, Tidor B.

J Phys Chem B. 2012 Mar 8;116(9):2891-904. doi: 10.1021/jp2068123. Epub 2012 Feb 22.

20.

Modeling formalisms in Systems Biology.

Machado D, Costa RS, Rocha M, Ferreira EC, Tidor B, Rocha I.

AMB Express. 2011 Dec 5;1:45. doi: 10.1186/2191-0855-1-45.

21.

Delineation of lipopolysaccharide (LPS)-binding sites on hemoglobin: from in silico predictions to biophysical characterization.

Bahl N, Du R, Winarsih I, Ho B, Tucker-Kellogg L, Tidor B, Ding JL.

J Biol Chem. 2011 Oct 28;286(43):37793-803. doi: 10.1074/jbc.M111.245472. Epub 2011 Sep 6.

22.

Simulating EGFR-ERK signaling control by scaffold proteins KSR and MP1 reveals differential ligand-sensitivity co-regulated by Cbl-CIN85 and endophilin.

Huang L, Pan CQ, Li B, Tucker-Kellogg L, Tidor B, Chen Y, Low BC.

PLoS One. 2011;6(8):e22933. doi: 10.1371/journal.pone.0022933. Epub 2011 Aug 1.

23.

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

Hagen DR, Apgar JF, Witmer DK, White FM, Tidor B.

Mol Biosyst. 2011 Aug 1;7(8):2523-2524. No abstract available.

24.

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

Huggins DJ, Tidor B.

Protein Eng Des Sel. 2011 Oct;24(10):777-89. doi: 10.1093/protein/gzr036. Epub 2011 Jul 19.

25.

An integrated mathematical model of thrombin-, histamine-and VEGF-mediated signalling in endothelial permeability.

Wei XN, Han BC, Zhang JX, Liu XH, Tan CY, Jiang YY, Low BC, Tidor B, Chen YZ.

BMC Syst Biol. 2011 Jul 15;5:112. doi: 10.1186/1752-0509-5-112.

26.

Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control.

Leonard E, Ajikumar PK, Thayer K, Xiao WH, Mo JD, Tidor B, Stephanopoulos G, Prather KL.

Proc Natl Acad Sci U S A. 2010 Aug 3;107(31):13654-9. doi: 10.1073/pnas.1006138107. Epub 2010 Jul 19.

27.

Cellular level models as tools for cytokine design.

Radhakrishnan ML, Tidor B.

Biotechnol Prog. 2010 Jul-Aug;26(4):919-37. doi: 10.1002/btpr.387.

28.

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

Apgar JF, Witmer DK, White FM, Tidor B.

Mol Biosyst. 2010 Oct;6(10):1890-900. doi: 10.1039/b918098b. Epub 2010 Jun 17.

29.

Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance.

Nalam MN, Ali A, Altman MD, Reddy GS, Chellappan S, Kairys V, Ozen A, Cao H, Gilson MK, Tidor B, Rana TM, Schiffer CA.

J Virol. 2010 May;84(10):5368-78. doi: 10.1128/JVI.02531-09. Epub 2010 Mar 17.

30.

SENSITIVITY ANALYSIS FOR OSCILLATING DYNAMICAL SYSTEMS.

Wilkins AK, Tidor B, White J, Barton PI.

SIAM J Sci Comput. 2009 Jun;31(4):2706-2732.

31.

CHARMM: the biomolecular simulation program.

Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M.

J Comput Chem. 2009 Jul 30;30(10):1545-614. doi: 10.1002/jcc.21287. Review.

32.

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

Cosgrove BD, King BM, Hasan MA, Alexopoulos LG, Farazi PA, Hendriks BS, Griffith LG, Sorger PK, Tidor B, Xu JJ, Lauffenburger DA.

Toxicol Appl Pharmacol. 2009 Jun 15;237(3):317-30. doi: 10.1016/j.taap.2009.04.002. Epub 2009 Apr 9.

33.

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

King BM, Tidor B.

Bioinformatics. 2009 May 1;25(9):1165-72. doi: 10.1093/bioinformatics/btp109. Epub 2009 Mar 4.

34.

Additivity in the analysis and design of HIV protease inhibitors.

Jorissen RN, Reddy GS, Ali A, Altman MD, Chellappan S, Anjum SG, Tidor B, Schiffer CA, Rana TM, Gilson MK.

J Med Chem. 2009 Feb 12;52(3):737-54. doi: 10.1021/jm8009525.

35.

Symmetric signaling by an asymmetric 1 erythropoietin: 2 erythropoietin receptor complex.

Zhang YL, Radhakrishnan ML, Lu X, Gross AW, Tidor B, Lodish HF.

Mol Cell. 2009 Jan 30;33(2):266-74. doi: 10.1016/j.molcel.2008.11.026.

36.

Distinct mechanisms act in concert to mediate cell cycle arrest.

Toettcher JE, Loewer A, Ostheimer GJ, Yaffe MB, Tidor B, Lahav G.

Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):785-90. doi: 10.1073/pnas.0806196106. Epub 2009 Jan 12.

37.

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

Hong EJ, Lippow SM, Tidor B, Lozano-Pérez T.

J Comput Chem. 2009 Sep;30(12):1923-45. doi: 10.1002/jcc.21188.

38.
39.

Aglycosylated immunoglobulin G1 variants productively engage activating Fc receptors.

Sazinsky SL, Ott RG, Silver NW, Tidor B, Ravetch JV, Wittrup KD.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20167-72. doi: 10.1073/pnas.0809257105. Epub 2008 Dec 12.

40.

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

Huggins DJ, Altman MD, Tidor B.

Proteins. 2009 Apr;75(1):168-86. doi: 10.1002/prot.22226.

41.
42.

Optimal drug cocktail design: methods for targeting molecular ensembles and insights from theoretical model systems.

Radhakrishnan ML, Tidor B.

J Chem Inf Model. 2008 May;48(5):1055-73. doi: 10.1021/ci700452r. Epub 2008 May 27.

43.

Evaluation of electrostatic interactions.

Green DF, Tidor B.

Curr Protoc Bioinformatics. 2003 Aug;Chapter 8:Unit 8.3. doi: 10.1002/0471250953.bi0803s02.

PMID:
18428710
44.

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

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.

J Am Chem Soc. 2008 May 14;130(19):6099-113. doi: 10.1021/ja076558p. Epub 2008 Apr 16.

45.

Novel method for probing the specificity binding profile of ligands: applications to HIV protease.

Sherman W, Tidor B.

Chem Biol Drug Des. 2008 May;71(5):387-407. doi: 10.1111/j.1747-0285.2008.00659.x. Epub 2008 Mar 31.

46.

Stimulus design for model selection and validation in cell signaling.

Apgar JF, Toettcher JE, Endy D, White FM, Tidor B.

PLoS Comput Biol. 2008 Feb;4(2):e30. doi: 10.1371/journal.pcbi.0040030.

47.

The Per2 negative feedback loop sets the period in the mammalian circadian clock mechanism.

Wilkins AK, Barton PI, Tidor B.

PLoS Comput Biol. 2007 Dec;3(12):e242.

48.

Computationally mapping sequence space to understand evolutionary protein engineering.

Armstrong KA, Tidor B.

Biotechnol Prog. 2008 Jan-Feb;24(1):62-73. Epub 2007 Nov 17.

49.
50.

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

Lipovsek D, Antipov E, Armstrong KA, Olsen MJ, Klibanov AM, Tidor B, Wittrup KD.

Chem Biol. 2007 Oct;14(10):1176-85.

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