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	CIRSE: A solvation energy estimator compatible with flexible protein docking and design applications [My Copy] Protein Sci, Vol. 15, No. 7. (1 July 2006), pp. 1579-1596. by David S. Cerutti, Tushar Jain, Andrew J. Mccammon posted to no-tag by dfgreen on 2009-01-08 21:20:08 as along with 1 person qwermish
	Dead-end elimination with backbone flexibility. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 13. (1 July 2007) by I. Georgiev, B. R. Donald posted to no-tag by dfgreen on 2009-01-08 22:12:14 as along with 1 person carlk
	The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Ivelin Georgiev, Ryan H. Lilien, Bruce R. Donald posted to no-tag by dfgreen on 2009-01-08 22:11:58 as along with 2 people RamuAnandakrishnan carlk
	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
	Algorithm for backrub motions in protein design [My Copy] Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i196-204. by Ivelin Georgiev, Daniel Keedy, Jane S. Richardson, David C. Richardson, Bruce R. Donald posted to no-tag by dfgreen on 2009-01-08 21:50:22 as along with 2 people hmk jwm
	Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction. [My Copy] Biopolymers, Vol. 50, No. 2. (August 1999), pp. 111-131. by J. Mendes, C. M. Soares, M. A. Carrondo posted to no-tag by dfgreen on 2009-01-08 21:19:43 as
	Protein design by binary patterning of polar and nonpolar amino acids [My Copy] Science, Vol. 262, No. 5140. (10 December 1993), pp. 1680-1685. by S. Kamtekar, J. M. Schiffer, H. Xiong, J. M. Babik, M. H. Hecht posted to no-tag by dfgreen on 2009-01-08 21:15:38 as
	A Hierarchical Approach for Parallelization of a Global Optimization Method for Protein Structure Prediction [My Copy] Euro-Par’99 Parallel Processing (1999), pp. 579-585. by S. Crivelli, T. Head-Gordon, R. Byrd, E. Eskow, R. Schnabel posted to no-tag by dfgreen on 2009-01-08 21:14:59 as
	The Thermodynamics of Protein-Ligand Interaction and Solvation: Insights for Ligand Design. [My Copy] Journal of molecular biology (9 October 2008) by Tjelvar S G S. Olsson, Mark A A. Williams, William R R. Pitt, John E E. Ladbury posted to no-tag by dfgreen on 2009-01-08 20:28:35 as along with 4 people and 1 group nickolay min013 higueruelo barry McCammon
	Carbohydrate-Protein Recognition: Molecular Dynamics Simulations and Free Energy Analysis of Oligosaccharide Binding to Concanavalin A [My Copy] Biophys. J., Vol. 81, No. 3. (1 September 2001), pp. 1373-1388. by R. A. Bryce, I. H. Hillier, J. H. Naismith posted to no-tag by dfgreen on 2009-01-08 17:17:03 as along with 1 person papatonyhill
	Evaluation of Models of Electrostatic Interactions in Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 107, No. 9. (1 March 2003), pp. 2075-2090. by Alexandre V. Morozov, Tanja Kortemme, David Baker posted to electrostatics by dfgreen on 2009-01-07 23:38:57 as
	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
	Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 14. (15 July 2006) by I. Georgiev, R. H. Lilien, B. R. Donald posted to no-tag by dfgreen on 2009-01-08 22:13:10 as along with 1 person carlk
	Dead-end elimination for multistate protein design. [My Copy] Journal of computational chemistry, Vol. 28, No. 13. (October 2007), pp. 2122-2129. by C. Yanover, M. Fromer, J. M. Shifman posted to no-tag by dfgreen on 2009-01-08 22:12:32 as along with 1 person carlk
	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
	Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization. [My Copy] Proteins, Vol. 48, No. 1. (1 July 2002), pp. 31-43. by J. Desmet, J. Spriet, I. Lasters posted to no-tag by dfgreen on 2009-01-08 22:03:30 as
	Computation of the binding of fully flexible peptides to proteins with flexible side chains. [My Copy] The FASEB journal : official publication of the Federation of American Societies for Experimental Biology, Vol. 11, No. 2. (February 1997), pp. 164-172. by J. Desmet, I. A. Wilson, M. Joniau, M. De Maeyer, I. Lasters posted to no-tag by dfgreen on 2009-01-08 22:03:07 as
	The fuzzy-end elimination theorem: correctly implementing the side chain placement algorithm based on the dead-end elimination theorem. [My Copy] Protein engineering, Vol. 6, No. 7. (September 1993), pp. 717-722. by I. Lasters, J. Desmet posted to no-tag by dfgreen on 2009-01-08 22:02:17 as along with 1 person carlk
	The dead-end elimination method, tryptophan rotamers, and fluorescence lifetimes. [My Copy] Biophysical journal, Vol. 85, No. 3. (September 2003), pp. 1894-1902. by M. Hellings, M. De Maeyer, S. Verheyden, et al.Q. Hao, E. J. Van Damme, W. J. Peumans, Y. Engelborghs posted to no-tag by dfgreen on 2009-01-08 21:51:32 as
	De novo design of the hydrophobic core of ubiquitin. [My Copy] Protein science : a publication of the Protein Society, Vol. 6, No. 6. (June 1997), pp. 1167-1178. by G. A. Lazar, J. R. Desjarlais, T. M. Handel posted to no-tag by dfgreen on 2009-01-08 21:28:08 as
	A hierarchical approach to protein molecular evolution. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 6. (16 March 1999), pp. 2591-2595. by L. D. Bogarad, M. W. Deem posted to no-tag by dfgreen on 2009-01-08 21:14:19 as along with 2 people Sylvain_Prigent tomhebbron
	Dissecting protein-RNA recognition sites [My Copy] Nucl. Acids Res., Vol. 36, No. 8. (19 March 2008), pp. gkn102-2716. by Ranjit P. Bahadur, Martin Zacharias, Joel Janin posted to no-tag by dfgreen on 2009-01-08 20:59:00 as along with 6 people and 1 group balewis aditi9783 svozil zhouyu marck inesdesantiago Bioinformatics
	Dissecting protein-protein recognition sites [My Copy] Proteins: Structure, Function, and Genetics, Vol. 47, No. 3. (2002), pp. 334-343. by Pinak Chakrabarti, Joël Janin posted to interactions protein-protein by dfgreen on 2009-01-08 20:58:41 as along with 1 person and 1 group csrocha structural_bioinformatics
	Molecular dynamics and free energy analysis of neuraminidase-ligand interactions. [My Copy] Protein science : a publication of the Protein Society, Vol. 13, No. 4. (April 2004), pp. 946-957. by P. Bonnet, R. A. Bryce posted to no-tag by dfgreen on 2009-01-08 20:50:52 as along with 1 person GermanErlenkamp
	Dependence of Hydration Free Energy on Solute Size [My Copy] The Journal of Physical Chemistry, Vol. 100, No. 4. (1 January 1996), pp. 1323-1329. by John Perkyns, Montgomery B. Pettitt posted to no-tag by dfgreen on 2009-01-08 20:47:40 as
	Microscopic theory of the dielectric properties of proteins. [My Copy] Biophysical journal, Vol. 59, No. 3. (March 1991), pp. 670-690. by T. Simonson, D. Perahia, A. T. Brünger posted to no-tag by dfgreen on 2009-01-08 03:15:33 as along with 1 person dimka
	MM-PBSA free energy analysis of endo-1,4-xylanase II (XynII)-substrate complexes: binding of the reactive sugar in a skew boat and chair conformation. [My Copy] Organic & biomolecular chemistry, Vol. 1, No. 20. (21 October 2003), pp. 3535-3540. by T. Laitinen, J. Rouvinen, M. Peräkylä posted to no-tag by dfgreen on 2009-01-08 03:02:38 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
	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
	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
	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
	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
	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
	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
	An extended dead-end elimination algorithm to determine gap-free lists of low energy states. [My Copy] Journal of computational chemistry, Vol. 28, No. 14. (15 November 2007), pp. 2325-2335. by E. Kloppmann, G. M. Ullmann, T. Becker posted to no-tag by dfgreen on 2009-01-08 22:12:53 as
	Theoretical and algorithmical optimization of the dead-end elimination theorem. [My Copy] Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (1997), pp. 122-133. by J. Desmet, M. De Maeyer, I. Lasters posted to no-tag by dfgreen on 2009-01-08 22:02:52 as
	Residue-rotamer-reduction algorithm for the protein side-chain conformation problem [My Copy] Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 188-194. by Wei Xie, Nikolaos V. Sahinidis posted to no-tag by dfgreen on 2009-01-08 21:52:51 as along with 4 people and 2 groups bicko marcius bluvsh1 carlk BioinfoCIPF SGU-CIPF
	Designed protein G core variants fold to native-like structures: sequence selection by ORBIT tolerates variation in backbone specification. [My Copy] Protein science : a publication of the Protein Society, Vol. 10, No. 2. (February 2001), pp. 450-454. by S. A. Ross, C. A. Sarisky, A. Su, S. L. Mayo posted to no-tag by dfgreen on 2009-01-08 21:49:49 as
	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
	Potentials of mean force for the interaction of blocked alanine dipeptide molecules in water and gas phase from MD simulations. [My Copy] Biophysical journal, Vol. 89, No. 3. (September 2005), pp. 1433-1445. by V. M. Dadarlat posted to no-tag by dfgreen on 2009-01-08 20:38:29 as
	Entropic Contributions to Free Energies of Solvation [My Copy] The Journal of Physical Chemistry, Vol. 98, No. 15. (1 April 1994), pp. 4141-4147. by David J. Giesen, Christopher J. Cramer, Donald G. Truhlar posted to hydrophobic solvation by dfgreen on 2009-01-08 20:27:01 as
	Role of backbone solvation in determining thermodynamic β propensities of the amino acids [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 3. (5 February 2002), pp. 1309-1313. by Franc Avbelj, Robert L. Baldwin posted to no-tag by dfgreen on 2009-01-08 20:15:45 as
	Apolar and polar solvation thermodynamics related to the protein unfolding process. [My Copy] Biophysical journal, Vol. 82, No. 2. (February 2002), pp. 713-719. by A. Bakk, J. S. Høye, A. Hansen posted to no-tag by dfgreen on 2009-01-08 20:15:03 as
	Biomolecular electrostatics with the linearized Poisson-Boltzmann equation. [My Copy] Biophysical journal, Vol. 76, No. 1 Pt 1. (January 1999), pp. 1-16. by F. Fogolari, P. Zuccato, G. Esposito, P. Viglino posted to no-tag by dfgreen on 2009-01-08 19:11:47 as along with 2 people csrocha lillekatt
	Electrostatics in biomolecular structure and dynamics [My Copy] Chemical Reviews, Vol. 90, No. 3. (1 May 1990), pp. 509-521. by Malcolm E. Davis, J. Andrew Mccammon posted to dynamics electrostatics molecular protein review by dfgreen on 2009-01-08 19:08:08 as along with 2 people scampos flbarroso
	Free Energy Simulations Come of Age: Protein−Ligand Recognition [My Copy] Accounts of Chemical Research, Vol. 35, No. 6. (1 June 2002), pp. 430-437. by Thomas Simonson, Georgios Archontis, Martin Karplus posted to no-tag by dfgreen on 2009-01-08 18:25:25 as along with 2 people flbarroso dmobley
	Determination of pKas of ionizable groups in proteins: the pKa of Glu 7 and 35 in hen eggs white lysozyme and Glu 106 in human carbonic anhydrase II [My Copy] Journal of the American Chemical Society, Vol. 113, No. 9. (1 April 1991), pp. 3572-3575. by Kenneth M. Merz posted to no-tag by dfgreen on 2009-01-08 18:12:39 as
	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

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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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