dfgreen's Tidor:B [36 articles] Export

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	Rotamer optimization for protein design through MAP estimation and problem-size reduction. [My Copy] Journal of computational chemistry (2 January 2009) by Eun-Jong J. Hong, Shaun M M. Lippow, Bruce Tidor, Tomás Lozano-Pérez posted to no-tag by dfgreen on 2009-01-08 22:11:33 as
	Evaluation of an inverse molecular design algorithm in a model binding site [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by David J. Huggins, Michael D. Altman, Bruce Tidor posted to no-tag by dfgreen on 2009-01-08 22:11:16 as along with 3 people and 2 groups mijam barry middledomain structural_bioinformatics McCammon
	Optimization of electrostatic binding free energy [My Copy] The Journal of Chemical Physics, Vol. 106, No. 21. (1997), pp. 8681-8690. by Lee P. Lee, Bruce Tidor posted to binding electrostatics ligand optimization by dfgreen on 2009-01-08 17:34:16 as
	Electrostatic specificity in molecular ligand design [My Copy] The Journal of Chemical Physics, Vol. 112, No. 20. (2000), pp. 9120-9131. by Erik Kangas, Bruce Tidor posted to binding electrostatics ligand optimization specificity by dfgreen on 2009-01-08 17:32:10 as
	Optimizing electrostatic affinity in ligand--receptor binding: Theory, computation, and ligand properties [My Copy] The Journal of Chemical Physics, Vol. 109, No. 17. (1998), pp. 7522-7545. by Erik Kangas, Bruce Tidor posted to binding electrostatics ligand optimization by dfgreen on 2009-01-08 17:28:02 as
	Hidden thermodynamics of mutant proteins: a molecular dynamics analysis [My Copy] Science, Vol. 244, No. 4908. (2 June 1989), pp. 1069-1072. by J. Gao, K. Kuczera, B. Tidor, M. Karplus posted to dynamics free-energy molecular perturbation protein stability by dfgreen on 2009-01-08 14:04:19 as
	Free energy of sickling: A simulation analysis [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 87, No. 21. (November 1990), pp. 8481-8485. by K. Kuczera, J. Gao, B. Tidor, M. Karplus posted to dynamics free-energy molecular perturbation by dfgreen on 2009-01-08 14:01:43 as
	Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 88, No. 23. (1 December 1991), pp. 10880-10884. by M. Prevost, S. J. Wodak, B. Tidor, M. Karplus posted to dynamics effect hydrophobic molecular protein stability by dfgreen on 2009-01-08 13:59:36 as
	The Per2 negative feedback loop sets the period in the mammalian circadian clock mechanism. [My Copy] PLoS computational biology, Vol. 3, No. 12. (1 December 2007), e242. by Katharina A. Wilkins, Paul I. Barton, Bruce Tidor posted to biology systems by dfgreen on 2009-01-08 01:54:34 as along with 2 people Biomedyknight cdppublications
	Design of Mutation-resistant HIV Protease Inhibitors with the Substrate Envelope Hypothesis [My Copy] Chemical Biology & Drug Design, Vol. 69, No. 5. (May 2007), pp. 298-313. by Sripriya Chellappan, Kiran Kumar Reddy, Akbar Ali, et al.Madhavi N. L. Nalam, Saima G. Anjum, Hong Cao, Visvaldas Kairys, Miguel X. Fernandes, Michael D. Altman, Bruce Tidor, Tariq M. Rana, Celia A. Schiffer, Michael K. Gilson posted to binding design ligand resistance by dfgreen on 2009-01-08 01:53:07 as along with 1 person and 1 group cdppublications CDP
	The Contribution of Vibrational Entropy to Molecular Association : The Dimerization of Insulin [My Copy] Journal of Molecular Biology, Vol. 238, No. 3. (5 May 1994), pp. 405-414. by Bruce Tidor, Martin Karplus posted to binding entropy harmonics protein vibrational by dfgreen on 2009-01-08 01:46:57 as along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
	Repacking protein cores with backbone freedom: structure prediction for coiled coils. [My Copy] Proc Natl Acad Sci U S A, Vol. 92, No. 18. (29 August 1995), pp. 8408-8412. by P. B. Harbury, B. Tidor, P. S. Kim posted to design packing protein by dfgreen on 2009-01-08 01:43:13 as along with 3 people kgutwin oteri bethbromley
	Barstar is electrostatically optimized for tight binding to barnase. [My Copy] Nature structural biology, Vol. 8, No. 1. (January 2001), pp. 73-76. by L. P. Lee, B. Tidor posted to binding electrostatics interactions optimization protein protein-protein by dfgreen on 2009-01-08 01:40:32 as along with 1 person flbarroso
	Computational design of antibody-affinity improvement beyond in vivo maturation. [My Copy] Nat Biotechnol (23 September 2007) by Shaun M M. Lippow, K Dane D. Wittrup, Bruce Tidor posted to binding design electrostatics interactions protein protein-protein by dfgreen on 2009-01-08 01:33:59 as along with 4 people and 1 group Scis0000002 kirasato hmk zwang Chang group
	Rational cytokine design for increased lifetime and enhanced potency using pH-activated "histidine switching" [My Copy] Nat Biotech, Vol. 20, No. 9. (2002), pp. 908-913. by Casim A. Sarkar, Ky Lowenhaupt, Thomas Horan, Thomas C. Boone, Bruce Tidor, Douglas A. Lauffenburger posted to biology electrostatics engineering protein systems by dfgreen on 2009-01-08 01:29:49 as along with 1 person tklee
	Effects of salt bridges on protein structure and design. [My Copy] Protein science : a publication of the Protein Society, Vol. 7, No. 9. (September 1998), pp. 1898-1914. by C. V. Sindelar, Z. S. Hendsch, B. Tidor posted to design electrostatics protein stability by dfgreen on 2009-01-08 01:26:52 as
	Escherichia coli Glutaminyl-tRNA Synthetase is Electrostatically Optimized for Binding of its Cognate Substrates [My Copy] Journal of Molecular Biology, Vol. 342, No. 2. (10 September 2004), pp. 435-452. by D. F. Green, B. Tidor posted to binding electrostatics ligand optimization by dfgreen on 2009-01-08 01:19:42 as
	Do salt bridges stabilize proteins? A continuum electrostatic analysis. [My Copy] Protein science : a publication of the Protein Society, Vol. 3, No. 2. (February 1994), pp. 211-226. by Z. S. Hendsch, B. Tidor posted to electrostatics protein stability by dfgreen on 2009-01-08 01:17:27 as along with 1 person flbarroso
	Computation of electrostatic complements to proteins: a case of charge stabilized binding. [My Copy] Protein science : a publication of the Protein Society, Vol. 7, No. 1. (January 1998), pp. 206-210. by L. T. Chong, S. E. Dempster, Z. S. Hendsch, L. P. Lee, B. Tidor posted to binding electrostatics optimization protein by dfgreen on 2009-01-08 01:14:58 as
	Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding. [My Copy] Protein science : a publication of the Protein Society, Vol. 8, No. 7. (July 1999), pp. 1381-1392. by Z. S. Hendsch, B. Tidor posted to binding electrostatics interactions protein protein-protein by dfgreen on 2009-01-08 01:13:00 as
	Charge optimization leads to favorable electrostatic binding free energy. [My Copy] Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics, Vol. 59, No. 5 Pt B. (May 1999), pp. 5958-5961. by E. Kangas, B. Tidor posted to binding electrostatics ligand optimization by dfgreen on 2009-01-08 01:11:00 as along with 1 person flbarroso
	Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex. [My Copy] Protein science : a publication of the Protein Society, Vol. 10, No. 2. (February 2001), pp. 362-377. by L. P. Lee, B. Tidor posted to binding electrostatics optimization protein by dfgreen on 2009-01-07 23:35:10 as along with 2 people flbarroso ras
	Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface. [My Copy] Proteins, Vol. 60, No. 4. (1 September 2005), pp. 644-657. by D. F. Green, B. Tidor posted to binding electrostatics optimization protein by dfgreen on 2009-01-07 23:24:29 as along with 1 person boris_aguilar
	Action-at-a-distance interactions enhance protein binding affinity. [My Copy] Protein science : a publication of the Protein Society, Vol. 14, No. 5. (May 2005), pp. 1363-1369. by B. A. Joughin, D. F. Green, B. Tidor posted to action-at-a-distance binding electrostatics protein by dfgreen on 2009-01-07 23:19:09 as along with 1 person Lombardo_7
	Parameter Dependence in Continuum Electrostatic Calculations: A Study Using Protein Salt Bridges [My Copy] The Journal of Physical Chemistry B, Vol. 102, No. 22. (1 May 1998), pp. 4404-4410. by Zachary S. Hendsch, Charles V. Sindelar, Bruce Tidor posted to electrostatics by dfgreen on 2009-01-07 20:58:23 as along with 1 person onufriev
	Simulation analysis of the stability mutant R96H of T4 lysozyme [My Copy] Biochemistry, Vol. 30, No. 13. (1 April 1991), pp. 3217-3228. by Bruce Tidor, Martin Karplus posted to dynamics molecular protein stability by dfgreen on 2009-01-07 20:56:57 as
	High-Resolution Protein Design with Backbone Freedom [My Copy] Science, Vol. 282, No. 5393. (20 November 1998), pp. 1462-1467. by Pehr B. Harbury, Joseph J. Plecs, Bruce Tidor, Tom Alber, Peter S. Kim posted to design protein by dfgreen on 2009-01-07 20:52:27 as along with 2 people kgutwin apaydin
	Protein Stabilization by Removal of Unsatisfied Polar Groups: Computational Approaches and Experimental Tests† [My Copy] Biochemistry, Vol. 35, No. 24. (1 January 1996), pp. 7621-7625. by Zachary S. Hendsch, Thorlakur Jonsson, Robert T. Sauer, Bruce Tidor posted to electrostatics engineering protein by dfgreen on 2009-01-07 20:50:46 as
	Evaluation of ab Initio Charge Determination Methods for Use in Continuum Solvation Calculations [My Copy] J. Phys. Chem. B, Vol. 107, No. 37. (18 September 2003), pp. 10261-10273. by D. F. Green, B. Tidor posted to ab-initio charges electrostatics quantum-mechanics solvation by dfgreen on 2009-01-07 20:39:07 as along with 1 person loison
	Preferential Heterodimer Formation via Undercompensated Electrostatic Interactions [My Copy] Journal of the American Chemical Society, Vol. 123, No. 6. (1 February 2001), pp. 1264-1265. by Zachary S. Hendsch, Michael J. Nohaile, Robert T. Sauer, Bruce Tidor posted to electrostatics specificity by dfgreen on 2009-01-07 20:35:05 as
	Rational Design of New Binding Specificity by Simultaneous Mutagenesis of Calmodulin and a Target Peptide† [My Copy] Biochemistry, Vol. 45, No. 41. (1 October 2006), pp. 12547-12559. by David F. Green, Andrew T. Dennis, Peter S. Fam, Bruce Tidor, Alan Jasanoff posted to design engineering protein specificity by dfgreen on 2009-01-07 20:31:30 as
	Electrostatic Complementarity at Ligand Binding Sites: Application to Chorismate Mutase [My Copy] J. Phys. Chem. B, Vol. 105, No. 4. (1 February 2001), pp. 880-888. by E. Kangas, B. Tidor posted to binding electrostatics ligand optimization by dfgreen on 2009-01-07 20:11:32 as along with 1 person dimka
	Long-Range Electrostatic Contributions to Protein−Ligand Binding Estimated Using Protein Charge Ladders, Affinity Capillary Electrophoresis, and Continuum Electrostatic Theory [My Copy] Journal of the American Chemical Society, Vol. 121, No. 18. (1 May 1999), pp. 4340-4347. by Justin A. Caravella, Jeffrey D. Carbeck, David C. Duffy, George M. Whitesides, Bruce Tidor posted to electrostatics by dfgreen on 2009-01-07 19:53:46 as
	Rational Modification of Protein Stability by the Mutation of Charged Surface Residues† [My Copy] Biochemistry, Vol. 39, No. 5. (1 February 2000), pp. 872-879. by Shari Spector, Minghui Wang, Stefan A. Carp, et al.James Robblee, Zachary S. Hendsch, Robert Fairman, Bruce Tidor, Daniel P. Raleigh posted to electrostatics engineering protein by dfgreen on 2009-01-07 19:49:09 as
	Altering dimerization specificity by changes in surface electrostatics [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 98, No. 6. (13 March 2001), pp. 3109-3114. by M. J. Nohaile, Z. S. Hendsch, B. Tidor, R. T. Sauer posted to electrostatics engineering protein specificity by dfgreen on 2009-01-07 19:40:29 as
	Evaluation of electrostatic interactions [My Copy] In Current Protocols in Bioinformatics (2003) by David F. Green, Bruce Tidor edited by G. E. Petsko posted to binding electrostatics optimization by dfgreen on 2009-01-07 18:52:02 as

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file-import-09-01-07b	274
electrostatics	96
protein	90
design	63
dynamics	47
molecular	47
ligand	46
solvation	44
binding	39
packing	19
quantum-mechanics	19
charges	18
optimization	18
free-energy	17
pka	17
interactions	17
review	17
perturbation	16
ab-initio	15
force-fields	15
generalized-born	13
hydrophobic	13
protein-protein	11
engineering	11
software	11
stability	9
specificity	9
structure	7
poisson-boltzmann	7
conformational	6
biopharmaceuticals	6
carbohydrate	6
enzyme	5
docking	5
catalysis	4
sequence	4
biology	4
preferences	4
systems	4
dna	4
homology	4
linear-programming	3
kinetics	3
entropy	3
semi-empirical	3
quadratic-programming	3
protonation	2
water	2
monte-carlo	2
visualization	2
structure-prediction	2
continuum-vdw	2
rna	2
folding	1
membrane-association	1
vibrational	1
calmodulin	1
phylogeny	1
resistance	1
hierarchicies	1
mean-field	1
rna-protein	1
harmonics	1
g-protein	1
dissociation	1
brownian	1
proteomics	1
analysis	1
action-at-a-distance	1
effect	1
atp	1
allostery	1
electrochemistry	1
text	1
senstivity	1

dfgreen's Tidor:B [36 articles] Export

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