dfgreen's library 585 articles Export

	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
	Automated protein structure homology modeling: a progress report. [My Copy] Pharmacogenomics, Vol. 5, No. 4. (June 2004), pp. 405-416. by J. Kopp, T. Schwede posted to homology protein review structure-prediction by dfgreen on 2009-01-09 02:53:00 as
	Protein structure prediction [My Copy] Current Opinion in Chemical Biology, Vol. 5, No. 1. (1 February 2001), pp. 51-56. by B. Al-Lazikani posted to homology protein review structure-prediction by dfgreen on 2009-01-09 02:51:34 as along with 2 people carlosjavierna granujilla
	Combinatorial protein biochemistry for therapeutics and proteomics. [My Copy] Current pharmaceutical biotechnology, Vol. 5, No. 1. (February 2004), pp. 17-27. by D. Lowe, L. Jermutus posted to biopharmaceuticals proteomics by dfgreen on 2009-01-09 02:14:38 as
	Newer monoclonal antibodies for hematological malignancies. [My Copy] Experimental hematology, Vol. 36, No. 7. (July 2008), pp. 755-768. by J. Castillo, E. Winer, P. Quesenberry posted to no-tag by dfgreen on 2009-01-09 02:13:29 as
	Monoclonal antibody therapy of haematological malignancies. [My Copy] BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy, Vol. 16, No. 4. (2002), pp. 283-301. by C. Dearden posted to biopharmaceuticals review by dfgreen on 2009-01-09 02:13:08 as
	Development of secreted proteins as biotherapeutic agents. [My Copy] Expert opinion on biological therapy, Vol. 4, No. 4. (April 2004), pp. 551-558. by A. L. Bonin-Debs, I. Boche, H. Gille, U. Brinkmann posted to biopharmaceuticals review by dfgreen on 2009-01-09 02:11:41 as
	Second-generation biopharmaceuticals [My Copy] European Journal of Pharmaceutics and Biopharmaceutics, Vol. 58, No. 2. (September 2004), pp. 185-196. by G. Walsh posted to biopharmaceuticals review by dfgreen on 2009-01-09 02:10:14 as along with 2 people 037418365 flbarroso
	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
	Comparison of simple potential functions for simulating liquid water [My Copy] The Journal of Chemical Physics, Vol. 79, No. 2. (1983), pp. 926-935. by William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, Michael L. Klein posted to force-fields monte-carlo water by dfgreen on 2009-01-09 02:01:48 as along with 17 people and 1 group jmparks fralium bmduggan kulinskii ibuch Lombardo_7 paddydu softsimu mleis ttjoseph ffranca easybakemuffin ashaytan RamuAnandakrishnan r2s2 pavanghatty Diego_Prada CMB
	A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model [My Copy] The Journal of Physical Chemistry, Vol. 97, No. 40. (1 October 1993), pp. 10269-10280. by Christopher I. Bayly, Piotr Cieplak, Wendy Cornell, Peter A. Kollman posted to ab-initio charges quantum-mechanics by dfgreen on 2009-01-09 02:00:35 as along with 2 people Scis0000002 paddydu
	Charges fit to electrostatic potentials. II. Can atomic charges be unambiguously fit to electrostatic potentials? [My Copy] Journal of Computational Chemistry, Vol. 17, No. 3. (1996), pp. 367-383. by Michelle M. Francl, Christina Carey, Lisa E. Chirlian, David M. Gange posted to ab-initio charges quantum-mechanics by dfgreen on 2009-01-09 01:57:32 as along with 2 people Scis0000002 flbarroso
	Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation [My Copy] Journal of the American Chemical Society, Vol. 115, No. 21. (1 October 1993), pp. 9620-9631. by Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, Peter A. Kollmann posted to ab-initio charges interactions quantum-mechanics solvation by dfgreen on 2009-01-09 01:55:58 as along with 1 person and 1 group A_Coletta_Thesis Structural Biology Group TorVergata
	Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis [My Copy] Journal of Computational Chemistry, Vol. 11, No. 3. (1990), pp. 361-373. by Curt M. Breneman, Kenneth B. Wiberg posted to ab-initio charges quantum-mechanics by dfgreen on 2009-01-09 01:54:39 as
	Electronic Population Analysis on LCAO[Single Bond]MO Molecular Wave Functions. I [My Copy] The Journal of Chemical Physics, Vol. 23, No. 10. (1955), pp. 1833-1840. by R. S. Mulliken posted to charges quantum-mechanics semi-empirical by dfgreen on 2009-01-09 01:41:08 as along with 4 people coomteng Scis0000002 pem tovrstra
	Determination of partial atomic charges from ab initio molecular electrostatic potentials. Application to formamide, methanol, and formic acid [My Copy] The Journal of Physical Chemistry, Vol. 82, No. 5. (1 March 1978), pp. 592-601. by Frank A. Momany posted to ab-initio charges quantum-mechanics by dfgreen on 2009-01-09 01:39:09 as
	Fitting Molecular Electrostatic Potentials from Quantum Mechanical Calculations [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 3. (1 May 2007), pp. 1004-1013. by Hao Hu, Zhenyu Lu, Weitao Yang posted to no-tag by dfgreen on 2009-01-09 01:37:24 as
	Atomic charges derived from electrostatic potentials: A detailed study [My Copy] Journal of Computational Chemistry, Vol. 8, No. 6. (1987), pp. 894-905. by Lisa E. Chirlian, Michelle M. Francl posted to ab-initio charges quantum-mechanics by dfgreen on 2009-01-09 01:36:47 as along with 1 person RamuAnandakrishnan
	An approach to computing electrostatic charges for molecules [My Copy] Journal of Computational Chemistry, Vol. 5, No. 2. (1984), pp. 129-145. by U. Chandra Singh, Peter A. Kollman posted to charges quantum-mechanics by dfgreen on 2009-01-08 23:38:08 as along with 4 people and 1 group whitead pavanghatty tovrstra kimikazu Jiang Research Group
	Atomic charges derived from semiempirical methods [My Copy] Journal of Computational Chemistry, Vol. 11, No. 4. (1990), pp. 431-439. by Brent H. Besler, Kenneth M. Merz, Peter A. Kollman posted to charges quantum-mechanics semi-empirical by dfgreen on 2009-01-08 23:36:06 as along with 1 person and 1 group A_Coletta_Thesis Structural Biology Group TorVergata
	Generation of OPLS-like charges from molecular electrostatic potential using restraints [My Copy] Journal of Computational Chemistry, Vol. 20, No. 5. (1999), pp. 483-498. by Richard H. Henchman, Jonathan W. Essex posted to ab-initio charges quantum-mechanics by dfgreen on 2009-01-08 23:34:56 as
	Free energies of hydration using restrained electrostatic potential derived charges via free energy perturbations and linear response [My Copy] Journal of Computational Chemistry, Vol. 20, No. 5. (1999), pp. 499-510. by Richard H. Henchman, Jonathan W. Essex posted to ab-initio charges free-energy perturbation quantum-mechanics solvation by dfgreen on 2009-01-08 23:33:59 as
	Effective atomic charges in alanine dipeptide [My Copy] Journal of Computational Chemistry, Vol. 20, No. 5. (1999), pp. 473-482. by J. Ridard, B. Lévy posted to ab-initio charges quantum-mechanics by dfgreen on 2009-01-08 23:30:09 as
	Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method [My Copy] Journal of Computational Chemistry, Vol. 21, No. 2. (2000), pp. 132-146. by Araz Jakalian, Bruce L. Bush, David B. Jack, Christopher I. Bayly posted to charges quantum-mechanics semi-empirical by dfgreen on 2009-01-08 23:29:06 as along with 1 person and 1 group sobolevnrm baker-group
	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
	Calculating the electrostatic potential of molecules in solution: Method and error assessment [My Copy] Journal of Computational Chemistry, Vol. 9, No. 4. (1988), pp. 327-335. by Michael K. Gilson, Kim A. Sharp, Barry H. Honig posted to electrostatics poisson-boltzmann software by dfgreen on 2009-01-08 23:13:27 as along with 2 people dmitry_s_yershov RamuAnandakrishnan
	Solving the finite difference linearized Poisson-Boltzmann equation: A comparison of relaxation and conjugate gradient methods [My Copy] Journal of Computational Chemistry, Vol. 10, No. 3. (1989), pp. 386-391. by M. E. Davis, J. A. Mccammon posted to no-tag by dfgreen on 2009-01-08 23:09:07 as along with 1 person dmitry_s_yershov
	Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations [My Copy] The Journal of Chemical Physics, Vol. 100, No. 12. (1994), pp. 9050-9063. by Dmitrii Beglov, Benoît Roux posted to dynamics molecular solvation by dfgreen on 2009-01-08 23:07:33 as along with 2 people dmitry_s_yershov jwagoner
	Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. [My Copy] Proteins, Vol. 4, No. 2. (1988), pp. 148-156. by A. T. Brünger, M. Karplus posted to interactions protonation software by dfgreen on 2009-01-08 22:59:43 as along with 1 person csrocha
	Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. [My Copy] J Mol Biol, Vol. 285, No. 4. (29 January 1999), pp. 1735-1747. by J. M. Word, S. C. Lovell, J. S. Richardson, D. C. Richardson posted to interactions packing protonation software by dfgreen on 2009-01-08 22:58:46 as along with 4 people and 2 groups kaarsinogen jwm j3xucite blackbart Radiation_Damage Stressosome
	VMD: visual molecular dynamics. [My Copy] Journal of molecular graphics, Vol. 14, No. 1. (February 1996) by W. Humphrey, A. Dalke, K. Schulten posted to software structure visualization by dfgreen on 2009-01-08 22:56:29 as along with 6 people bratwurst oceanwind gisle lna dimka dgront
	Scalable molecular dynamics with NAMD [My Copy] Journal of Computational Chemistry, Vol. 26, No. 16. (December 2005), pp. 1781-1802. by James C. Phillips, Rosemary Braun, Wei Wang, et al.James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kalé, Klaus Schulten posted to dynamics molecular software by dfgreen on 2009-01-08 22:55:21 as along with 19 people and 5 groups pjkiley flbarroso yxue r2s2 grondina rpetrenko oteri oceanwind vahmurk gisle dimka jwm ttjoseph sangeetha yoel_rf bilab wilsoros sobolevnrm ibuch Radiation_Damage Stressosome Bioinformatics insilicodrug baker-group
	Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes. [My Copy] J Comput Chem, Vol. 22, No. 15. (30 November 2001), pp. 1857-1879. by Michael Schaefer, Christian Bartels, Fabrice Leclerc, Martin Karplus posted to electrostatics generalized-born by dfgreen on 2009-01-08 22:54:23 as along with 1 person baaden
	A Comprehensive Analytical Treatment of Continuum Electrostatics [My Copy] The Journal of Physical Chemistry, Vol. 100, No. 5. (1 January 1996), pp. 1578-1599. by Michael Schaefer, Martin Karplus posted to electrostatics generalized-born by dfgreen on 2009-01-08 22:53:34 as along with 1 person boris_aguilar
	Calculation of electrostatic potentials in an enzyme active site [My Copy] Nature, Vol. 330, No. 6143. (5 November 1987), pp. 84-86. by Michael K. Gilson, Barry H. Honig posted to electrostatics poisson-boltzmann by dfgreen on 2009-01-08 22:52:32 as along with 1 person flbarroso
	PBEQ-Solver for online visualization of electrostatic potential of biomolecules [My Copy] Nucl. Acids Res. (28 May 2008), gkn314. by Sunhwan Jo, Miklos Vargyas, Judit Vasko-Szedlar, Benoit Roux, Wonpil Im posted to no-tag by dfgreen on 2009-01-08 22:51:36 as along with 3 people flbarroso neils sobolevnrm
	Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis [My Copy] Proteins: Structure, Function, and Genetics, Vol. 4, No. 1. (1988), pp. 7-18. by Michael K. Gilson, Barry Honig posted to binding electrostatics poisson-boltzmann solvation by dfgreen on 2009-01-08 22:50:19 as along with 1 person flbarroso
	Macroscopic models of aqueous solutions: biological and chemical applications [My Copy] The Journal of Physical Chemistry, Vol. 97, No. 6. (1 February 1993), pp. 1101-1109. by Barry Honig, Kim Sharp, An S. Yang posted to binding electrostatics poisson-boltzmann protein by dfgreen on 2009-01-08 22:49:05 as
	Electrostatic Interactions in Macromolecules: Theory and Applications [My Copy] Annual Review of Biophysics and Biophysical Chemistry, Vol. 19, No. 1. (1990), pp. 301-332. by K. A. Sharp, B. Honig posted to electrostatics poisson-boltzmann review by dfgreen on 2009-01-08 22:47:45 as along with 3 people scampos flbarroso RamuAnandakrishnan
	Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation [My Copy] The Journal of Physical Chemistry, Vol. 94, No. 19. (1990), pp. 7684-7692. by Kim A. Sharp, Barry Honig posted to electrostatics poisson-boltzmann solvation by dfgreen on 2009-01-08 22:46:01 as along with 2 people Elena_Zubova dmitry_s_yershov
	Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models [My Copy] The Journal of Physical Chemistry, Vol. 98, No. 7. (1 February 1994), pp. 1978-1988. by Doree Sitkoff, Kim A. Sharp, Barry Honig posted to electrostatics poisson-boltzmann solvation by dfgreen on 2009-01-08 22:45:17 as along with 4 people melo_mcr onufriev dmitry_s_yershov flbarroso
	CHARMM: A program for macromolecular energy, minimization, and dynamics calculations [My Copy] Journal of Computational Chemistry, Vol. 4, No. 2. (1983), pp. 187-217. by Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, Martin Karplus posted to dynamics force-fields molecular software by dfgreen on 2009-01-08 22:40:53 as along with 16 people ubcg08l flbarroso nickolay newton1234 kgutwin r2s2 rpetrenko oceanwind RamuAnandakrishnan tovrstra Lombardo_7 dgront mmuecke rabio saravan gisle
	Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. [My Copy] Journal of computational chemistry, Vol. 23, No. 13. (October 2002), pp. 1236-1243. by M. Kuttel, J. W. Brady, K. J. Naidoo posted to carbohydrate force-fields by dfgreen on 2009-01-08 22:39:23 as
	All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins† [My Copy] The Journal of Physical Chemistry B, Vol. 102, No. 18. (1 April 1998), pp. 3586-3616. by A. D. Mackerell, D. Bashford, M. Bellott, et al.R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-Mccarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus posted to force-fields by dfgreen on 2009-01-08 22:38:00 as along with 12 people jmparks dsmueller rpetrenko jrperillaj Diego_Prada oceanwind mkrishna timg dimka ttjoseph papatonyhill ssomani
	An all-atom empirical energy function for the simulation of nucleic acids [My Copy] Journal of the American Chemical Society, Vol. 117, No. 48. (1 December 1995), pp. 11946-11975. by Alexander D. Mackerell, Joanna Wiorkiewicz-Kuczera, Martin Karplus posted to force-fields by dfgreen on 2009-01-08 22:37:05 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

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