dfgreen's optimization [18 articles] Export

Recent papers added to dfgreen's library classified by the tag optimization. You can also see everyone's optimization.

	An Interior-Point Algorithm for Nonconvex Nonlinear Programming [My Copy] Computational Optimization and Applications, Vol. 13, No. 1. (21 April 1999), pp. 231-252. by Robert J. Vanderbei, David F. Shanno posted to linear-programming optimization quadratic-programming by dfgreen on 2009-01-08 23:20:27 as
	LOQO:an interior point code for quadratic programming [My Copy] Optimization Methods and Software, Vol. 11, No. 1. (1999), pp. 451-484. by Robert J. Vanderbei posted to linear-programming optimization quadratic-programming by dfgreen on 2009-01-08 23:18:12 as
	LOQO user's manual version 3.10 [My Copy] Optimization Methods and Software, Vol. 11, No. 1. (1999), pp. 485-514. by Robert J. Vanderbei posted to linear-programming optimization quadratic-programming by dfgreen on 2009-01-08 23:16:43 as
	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
	Optimizing Ligand Charges for Maximum Binding Affinity. A Solvated Interaction Energy Approach [My Copy] The Journal of Physical Chemistry B, Vol. 105, No. 4. (1 February 2001), pp. 889-899. by Traian Sulea, Enrico O. Purisima posted to binding electrostatics ligand optimization by dfgreen on 2009-01-08 14:10:50 as
	Charge optimization of the interface between protein kinases and their ligands. [My Copy] Journal of computational chemistry, Vol. 25, No. 11. (August 2004), pp. 1416-1429. by P. A. Sims, C. F. Wong, J. A. McCammon posted to binding electrostatics ligand optimization by dfgreen on 2009-01-08 13:12:44 as along with 1 person boris_aguilar
	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
	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
	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
	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
	Optimization of electrostatic interactions in protein-protein complexes. [My Copy] Biophysical journal, Vol. 93, No. 10. (15 November 2007), pp. 3340-3352. by K. Brock, K. Talley, K. Coley, P. Kundrotas, E. Alexov posted to binding electrostatics interactions optimization protein-protein by dfgreen on 2009-01-07 23:33:15 as along with 4 people and 1 group flbarroso timg choonpeng sobolevnrm baker-group
	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
	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
	Charge Optimization Increases the Potency and Selectivity of a Chorismate Mutase Inhibitor [My Copy] Journal of the American Chemical Society, Vol. 125, No. 19. (1 May 2003), pp. 5598-5599. by Ajay Mandal, Donald Hilvert posted to binding electrostatics ligand optimization by dfgreen on 2009-01-07 19:46:07 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
interactions	17
pka	17
review	17
perturbation	16
ab-initio	15
force-fields	15
generalized-born	13
hydrophobic	13
engineering	11
protein-protein	11
software	11
specificity	9
stability	9
poisson-boltzmann	7
structure	7
biopharmaceuticals	6
carbohydrate	6
conformational	6
docking	5
enzyme	5
biology	4
catalysis	4
dna	4
homology	4
preferences	4
sequence	4
systems	4
entropy	3
kinetics	3
linear-programming	3
quadratic-programming	3
semi-empirical	3
continuum-vdw	2
monte-carlo	2
protonation	2
rna	2
structure-prediction	2
visualization	2
water	2
action-at-a-distance	1
allostery	1
analysis	1
atp	1
brownian	1
calmodulin	1
dissociation	1
effect	1
electrochemistry	1
folding	1
g-protein	1
harmonics	1
hierarchicies	1
mean-field	1
membrane-association	1
phylogeny	1
proteomics	1
resistance	1
rna-protein	1
senstivity	1
text	1
vibrational	1

dfgreen's optimization [18 articles] Export

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