dfgreen's design [63 articles] Export

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	A geometric approach to macromolecule-ligand interactions. [My Copy] J Mol Biol, Vol. 161, No. 2. (25 October 1982), pp. 269-288. by I. D. Kuntz, J. M. Blaney, S. J. Oatley, R. Langridge, T. E. Ferrin posted to design docking ligand by dfgreen on 2009-01-09 02:59:20 as along with 3 people Diego_Prada BragilMassoud kazemi
	Computer design of bioactive molecules: a method for receptor-based de novo ligand design. [My Copy] Proteins, Vol. 11, No. 4. (1991), pp. 314-328. by J. B. Moon, W. J. Howe posted to design ligand by dfgreen on 2009-01-09 02:58:16 as
	Utility of homology models in the drug discovery process. [My Copy] Drug discovery today, Vol. 9, No. 15. (1 August 2004), pp. 659-669. by A. Hillisch, L. F. Pineda, R. Hilgenfeld posted to design homology ligand review by dfgreen on 2009-01-09 02:56:20 as
	Homology-based modelling of targets for rational drug design. [My Copy] Mini Rev Med Chem, Vol. 4, No. 7. (September 2004), pp. 793-804. by H. Wieman, K. Tøndel, E. Anderssen, F. Drabløs posted to design homology ligand review by dfgreen on 2009-01-09 02:54:57 as along with 1 person and 2 groups sangeetha Bioinformatics insilicodrug
	Rational and "irrational" design of proteins and their use in biotechnology. [My Copy] IUBMB life, Vol. 49, No. 3. (March 2000), pp. 181-187. by A. E. Nixon, S. M. Firestine posted to biopharmaceuticals design engineering protein review by dfgreen on 2009-01-09 02:08:13 as
	The dead-end elimination theorem and its use in protein side-chain positioning [My Copy] Nature, Vol. 356, No. 6369. (April 1992), pp. 539-542. by Johan Desmet, Marc D. Maeyer, Bart Hazes, Ignace Lasters posted to design packing protein by dfgreen on 2009-01-08 22:13:57 as along with 3 people dgront bluvsh1 mijam
	Molecular engineering: An approach to the development of general capabilities for molecular manipulation [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 78, No. 9. (1981), pp. 5275-5278. by Eric K. Drexler posted to design protein by dfgreen on 2009-01-08 21:54:36 as
	Molecular technology. Designing proteins and peptides. [My Copy] Nature, Vol. 301, No. 5897. (20 January 1983) by C. Pabo posted to design protein by dfgreen on 2009-01-08 21:53:44 as
	Efficient rotamer elimination applied to protein side-chains and related spin glasses. [My Copy] Biophys J, Vol. 66, No. 5. (May 1994), pp. 1335-1340. by R. F. Goldstein posted to design packing protein by dfgreen on 2009-01-08 21:49:12 as along with 6 people dgront bluvsh1 kazemi rsantana mijam carlk
	The dead-end elimination theorem: mathematical aspects, implementation, optimizations, evaluation, and performance. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 143 (2000), pp. 265-304. by M. De Maeyer, J. Desmet, I. Lasters posted to design protein by dfgreen on 2009-01-08 21:47:16 as
	Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains. [My Copy] Protein engineering, Vol. 8, No. 8. (August 1995), pp. 815-822. by I. Lasters, M. De Maeyer, J. Desmet posted to design packing protein by dfgreen on 2009-01-08 21:46:15 as along with 1 person carlk
	Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm. [My Copy] Proteins, Vol. 33, No. 2. (1 November 1998), pp. 227-239. by A. R. Leach, A. P. Lemon posted to design packing protein by dfgreen on 2009-01-08 21:45:23 as along with 2 people karinaecomp karbak
	De novo protein design: fully automated sequence selection. [My Copy] Science, Vol. 278, No. 5335. (3 October 1997), pp. 82-87. by B. I. Dahiyat, S. L. Mayo posted to design protein by dfgreen on 2009-01-08 21:44:08 as along with 4 people Lombardo_7 jwm medic0747 kevinchannon
	Protein design automation. [My Copy] Protein Sci, Vol. 5, No. 5. (May 1996), pp. 895-903. by B. I. Dahiyat, S. L. Mayo posted to design protein by dfgreen on 2009-01-08 21:43:17 as along with 4 people and 1 group jwm shuns nknii carlk TCR_Signaling
	Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination theorem [My Copy] Journal of Computational Chemistry, Vol. 19, No. 13. (1998), pp. 1505-1514. by Benjamin D. Gordon, Stephen L. Mayo posted to design protein by dfgreen on 2009-01-08 21:42:13 as along with 1 person mijam
	Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. [My Copy] J Mol Biol, Vol. 239, No. 2. (3 June 1994), pp. 249-275. by P. Koehl, M. Delarue posted to conformational design entropy packing protein by dfgreen on 2009-01-08 21:40:53 as along with 1 person bluvsh1
	De novo protein design. I. In search of stability and specificity. [My Copy] Journal of molecular biology, Vol. 293, No. 5. (12 November 1999), pp. 1161-1181. by P. Koehl, M. Levitt posted to design packing protein by dfgreen on 2009-01-08 21:40:02 as
	De novo protein design. II. Plasticity in sequence space. [My Copy] Journal of molecular biology, Vol. 293, No. 5. (12 November 1999), pp. 1183-1193. by P. Koehl, M. Levitt posted to design protein by dfgreen on 2009-01-08 21:39:08 as
	Structure-based conformational preferences of amino acids [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 22. (26 October 1999), pp. 12524-12529. by Patrice Koehl, Michael Levitt posted to conformational design packing preferences protein by dfgreen on 2009-01-08 21:37:57 as
	Prediction of protein side-chain conformation by packing optimization. [My Copy] Journal of molecular biology, Vol. 217, No. 2. (20 January 1991), pp. 373-388. by C. Lee, S. Subbiah posted to design packing protein by dfgreen on 2009-01-08 21:36:22 as
	Optimal Sequence Selection in Proteins of Known Structure by Simulated Evolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 91, No. 13. (21 June 1994), pp. 5803-5807. by H. W. Hellinga, F. M. Richards posted to design packing protein by dfgreen on 2009-01-08 21:34:53 as along with 2 people jwm msuarezdiez
	Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. [My Copy] J Mol Biol, Vol. 307, No. 1. (16 March 2001), pp. 429-445. by L. L. Looger, H. W. Hellinga posted to design packing protein by dfgreen on 2009-01-08 21:33:59 as along with 4 people and 1 group nknii dgront mijam carlk TCR_Signaling
	Computational design of receptor and sensor proteins with novel functions [My Copy] Nature, Vol. 423, No. 6936. (08 May 2003), pp. 185-190. by Loren L. Looger, Mary A. Dwyer, James J. Smith, Homme W. Hellinga posted to design engineering protein by dfgreen on 2009-01-08 21:32:41 as along with 4 people and 1 group dbikard whitead antonkratz dgront Jiang Research Group
	Protein Design: A Hierarchic Approach [My Copy] Science, Vol. 270, No. 5238. (10 November 1995), pp. 935-941. by James W. Bryson, Stephen F. Betz, Helen S. Lu, et al.Daniel J. Suich, Hongxing X. Zhou, Karyn T. O'Neil, William F. Degrado posted to design hierarchicies protein by dfgreen on 2009-01-08 21:31:51 as
	De novo protein design using pairwise potentials and a genetic algorithm [My Copy] Protein Sci, Vol. 3, No. 4. (1 April 1994), pp. 567-574. by D. T. Jones posted to design protein by dfgreen on 2009-01-08 21:29:49 as along with 1 person msuarezdiez
	De novo design of the hydrophobic cores of proteins. [My Copy] Protein Sci, Vol. 4, No. 10. (October 1995), pp. 2006-2018. by J. R. Desjarlais, T. M. Handel posted to design packing protein by dfgreen on 2009-01-08 21:27:26 as along with 3 people and 1 group oteri ashaytan chgjb Structural Biology Group TorVergata
	Solving and analyzing side-chain positioning problems using linear and integer programming [My Copy] Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 1028-1039. by Kingsford, Chazelle Bernard, Singh Mona posted to design packing protein by dfgreen on 2009-01-08 21:26:09 as along with 2 people apaydin bluvsh1
	Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model [My Copy] Proteins: Structure, Function, and Genetics, Vol. 37, No. 4. (1999), pp. 530-543. by Joaquim Mendes, António M. Baptista, Maria A. Carrondo, Cláudio M. Soares posted to design packing protein by dfgreen on 2009-01-08 21:23:04 as along with 2 people apaydin rsantana
	One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations. [My Copy] Protein science : a publication of the Protein Society, Vol. 14, No. 5. (May 2005), pp. 1293-1304. by S. A. Marshall, C. L. Vizcarra, S. L. Mayo posted to design electrostatics protein solvation by dfgreen on 2009-01-08 21:21:08 as
	Designing proteins for therapeutic applications. [My Copy] Current opinion in structural biology, Vol. 13, No. 4. (August 2003), pp. 513-518. by G. A. Lazar, S. A. Marshall, J. J. Plecs, S. L. Mayo, J. R. Desjarlais posted to biopharmaceuticals design engineering protein by dfgreen on 2009-01-08 21:18:13 as
	Design of a novel globular protein fold with atomic-level accuracy. [My Copy] Science (New York, N.Y.), Vol. 302, No. 5649. (21 November 2003), pp. 1364-1368. by Brian Kuhlman, Gautam Dantas, Gregory C. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker posted to design protein by dfgreen on 2009-01-08 21:16:44 as along with 10 people bmduggan kgutwin Diego_Prada onufriev apaydin jwm hmk heymiki kevinchannon ca3295
	Statistical theory for protein combinatorial libraries. packing interactions, backbone flexibility, and the sequence variability of a main-chain structure1 [My Copy] Journal of Molecular Biology, Vol. 306, No. 3. (23 February 2001), pp. 607-628. by Hidetoshi Kono, Jeffery G. Saven posted to design protein by dfgreen on 2009-01-08 21:12:43 as along with 3 people jwm kgutwin blackbart
	Computational design and characterization of a monomeric helical dinuclear metalloprotein. [My Copy] Journal of molecular biology, Vol. 334, No. 5. (12 December 2003), pp. 1101-1115. by J. R. Calhoun, H. Kono, S. Lahr, W. Wang, W. F. DeGrado, J. G. Saven posted to design engineering protein by dfgreen on 2009-01-08 21:11:36 as
	Computational redesign of endonuclease DNA binding and cleavage specificity [My Copy] Nature, Vol. 441, No. 7093. (1 June 2006), pp. 656-659. by Justin Ashworth, James J. Havranek, Carlos M. Duarte, et al.Django Sussman, Raymond J. Monnat, Barry L. Stoddard, David Baker posted to catalysis design engineering enzyme protein by dfgreen on 2009-01-08 21:10:19 as along with 4 people and 1 group apaydin aalibes jwm condon beta
	Computational design of water-soluble analogues of the potassium channel KcsA. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 7. (17 February 2004), pp. 1828-1833. by A. M. Slovic, H. Kono, J. D. Lear, J. G. Saven, W. F. DeGrado posted to design engineering protein by dfgreen on 2009-01-08 21:05:21 as along with 2 people hc5428 jwm
	A Ligand That Is Predicted to Bind Better to Avidin than Biotin: Insights from Computational Fluorine Scanning [My Copy] Journal of the American Chemical Society, Vol. 122, No. 16. (1 April 2000), pp. 3909-3916. by Bernd Kuhn, Peter A. Kollman posted to design dynamics electrostatics ligand molecular by dfgreen on 2009-01-08 18:37:36 as
	Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants. [My Copy] J Comput Aided Mol Des, Vol. 15, No. 8. (August 2001), pp. 721-740. by J. Mendes, A. M. Baptista, M. A. Carrondo, C. M. Soares posted to design mean-field protein solvation stability by dfgreen on 2009-01-08 18:35:31 as along with 1 person and 1 group nknii TCR_Signaling
	Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation. [My Copy] Protein science : a publication of the Protein Society, Vol. 13, No. 4. (April 2004), pp. 925-936. by N. Pokala, T. M. Handel posted to design electrostatics protein solvation by dfgreen on 2009-01-08 17:44:52 as
	Effective scoring function for protein sequence design. [My Copy] Proteins, Vol. 54, No. 2. (1 February 2004), pp. 271-281. by S. Liang, N. V. Grishin posted to design protein solvation by dfgreen on 2009-01-08 17:42:30 as
	Optimization and Computational Evaluation of a Series of Potential Active Site Inhibitors of the V82F/I84V Drug-resistant Mutant of HIV-1 Protease: an Application of the Relaxed Complex Method of Structure-based Drug Design [My Copy] Chemical Biology & Drug Design, Vol. 67, No. 5. (2006), pp. 336-345. by Alexander L. Perryman, Jung-Hsin Lin, J. A. Mccammon posted to design docking ligand by dfgreen on 2009-01-08 13:15:04 as along with 1 person aqeel
	Pairwise calculation of protein solvent-accessible surface areas. [My Copy] Folding & design, Vol. 3, No. 4. (1998), pp. 253-258. by A. G. Street, S. L. Mayo posted to design protein solvation by dfgreen on 2009-01-08 12:56:10 as along with 1 person hryk
	The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors. [My Copy] Journal of computer-aided molecular design, Vol. 12, No. 3. (May 1998), pp. 215-227. by R. J. Radmer, P. A. Kollman posted to binding design free-energy ligand perturbation by dfgreen on 2009-01-08 02:56:43 as
	Theoretical Studies Suggest a New Antifolate as a More Potent Inhibitor of Thymidylate Synthase [My Copy] Journal of the American Chemical Society, Vol. 122, No. 18. (1 May 2000), pp. 4385-4393. by Tai-Sung Lee, Peter A. Kollman posted to design dynamics free-energy ligand molecular perturbation by dfgreen on 2009-01-08 02:39:43 as
	Evolutionary algorithms in computer-aided molecular design. [My Copy] Journal of computer-aided molecular design, Vol. 10, No. 4. (August 1996), pp. 337-358. by D. E. Clark, D. R. Westhead posted to design ligand review by dfgreen on 2009-01-08 02:37:54 as
	Computational molecular modeling in peptide drug design. [My Copy] International journal of peptide and protein research, Vol. 44, No. 6. (December 1994), pp. 513-531. by G. V. Nikiforovich posted to design ligand review by dfgreen on 2009-01-08 02:35:13 as
	HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site. [My Copy] Proteins, Vol. 19, No. 3. (July 1994), pp. 199-221. by M. B. Eisen, D. C. Wiley, M. Karplus, R. E. Hubbard posted to design ligand by dfgreen on 2009-01-08 02:32:22 as
	Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs. [My Copy] Proteins, Vol. 29, No. 1. (September 1997), pp. 32-58. by D. Joseph-McCarthy, J. M. Hogle, M. Karplus posted to design ligand by dfgreen on 2009-01-08 02:30:51 as
	Automated site-directed drug design using molecular lattices. [My Copy] Journal of molecular graphics, Vol. 10, No. 2. (June 1992) by R. A. Lewis, D. C. Roe, C. Huang, T. E. Ferrin, R. Langridge, I. D. Kuntz posted to design ligand by dfgreen on 2009-01-08 02:24:53 as
	Functionality maps of binding sites: a multiple copy simultaneous search method. [My Copy] Proteins, Vol. 11, No. 1. (1991), pp. 29-34. by A. Miranker, M. Karplus posted to design interactions ligand molecular by dfgreen on 2009-01-08 02:23:03 as along with 1 person ubcg08l
	CAVEAT: a program to facilitate the design of organic molecules. [My Copy] Journal of computer-aided molecular design, Vol. 8, No. 1. (February 1994), pp. 51-66. by G. Lauri, P. A. Bartlett posted to design ligand by dfgreen on 2009-01-08 02:21:39 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 design [63 articles] Export

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