bilab's library 52 articles Export

	The Solvation Interface is a Determining Factor in Peptide Conformational Preferences [My Copy] Journal of Molecular Biology, Vol. 356, No. 1. (10 February 2006), pp. 248-256. by Eric J. Sorin, Young M. Rhee, Michael R. Shirts, Vijay S. Pande posted to folding by bilab on 2006-05-10 09:18:07 as
	Sub-microsecond Protein Folding [My Copy] Journal of Molecular Biology, Vol. In Press, Corrected Proof by Jan Kubelka, Thang K. Chiu, David R. Davies, William A. Eaton, James Hofrichter posted to folding by bilab on 2006-05-02 11:34:52 as
	Reaction coordinates and rates from transition paths. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 19. (10 May 2005), pp. 6732-6737. by Robert B. Best, Gerhard Hummer posted to folding by bilab on 2006-05-02 08:27:39 as along with 4 people allmensch apaydin mtw jlh64
	Exploring reaction pathways with transition path and umbrella sampling: application to methyl maltoside. [My Copy] J Chem Phys, Vol. 124, No. 11. (21 March 2006) by R. J. Dimelow, R. A. Bryce, A. J. Masters, I. H. Hillier, N. A. Burton posted to function by bilab on 2006-05-02 08:26:42 as along with 1 person ruvido
	In Silico Discovery of beta-Secretase Inhibitors. [My Copy] J Am Chem Soc, Vol. 128, No. 16. (26 April 2006), pp. 5436-5443. by D. Huang, U. Lüthi, P. Kolb, M. Cecchini, A. Barberis, A. Caflisch posted to function by bilab on 2006-05-02 08:24:02 as
	Network and graph analyses of folding free energy surfaces [My Copy] Current Opinion in Structural Biology In Protein-nucleic acid interactions/Folding and binding - Wei Yang and Gregory D Van Dyne/Mikael Oliveberg and Eugene I Shakhnovich, Vol. 16, No. 1. (February 2006), pp. 71-78. by Amedeo Caflisch posted to folding by bilab on 2006-05-02 08:23:26 as along with 5 people and 1 group barry apaydin mtw jlh64 Diego_Prada structural_bioinformatics
	Coupled folding and binding with alpha-helix-forming molecular recognition elements. [My Copy] Biochemistry, Vol. 44, No. 37. (20 September 2005), pp. 12454-12470. by C. J. Oldfield, Y. Cheng, M. S. Cortese, P. Romero, V. N. Uversky, A. K. Dunker posted to function by bilab on 2006-05-02 08:10:15 as
	Conformational Diversity of Ligands Bound to Proteins [My Copy] Journal of Molecular Biology, Vol. 356, No. 4. (3 March 2006), pp. 928-944. by Gareth R. Stockwell, Janet M. Thornton posted to docking by bilab on 2006-05-02 08:04:26 as along with 7 people JALumley ubcg08l BragilMassoud apaydin kuhn grottenolm thanatos
	A method for localizing ligand binding pockets in protein structures. [My Copy] Proteins, Vol. 62, No. 2. (1 February 2006), pp. 479-488. by F. Glaser, R. J. Morris, R. J. Najmanovich, R. A. Laskowski, J. M. Thornton posted to docking by bilab on 2006-05-02 08:03:08 as along with 4 people tjimenez nickolay sriram_s jwm
	Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. [My Copy] J Mol Biol, Vol. 345, No. 5. (4 February 2005), pp. 1281-1294. by O. Keskin, B. Ma, R. Nussinov posted to docking by bilab on 2006-05-02 08:01:36 as along with 9 people and 2 groups marti mdimmic ana barry baaden okarsligil bicko j3xucite xz structural_bioinformatics Bioinformatics
	Evolutionary trace report maker: a new type of service for comparative analysis of proteins. [My Copy] Bioinformatics (27 April 2006) by I Mihalek, I Res, O Lichtarge posted to evolution by bilab on 2006-05-02 05:51:24 as along with 1 person BragilMassoud
	Ribosome motions modulate electrostatic properties. [My Copy] Biopolymers, Vol. 74, No. 6. (15 August 2004), pp. 423-431. by J. Trylska, R. Konecny, F. Tama, C. L. Brooks, J. A. McCammon posted to function by bilab on 2006-05-01 18:07:16 as along with 1 person and 1 group anita structure-bii
	Symmetry, Form, and Shape: Guiding Principles for Robustness in Macromolecular Machines. [My Copy] Annu Rev Biophys Biomol Struct (13 January 2006) by Florence Tama, Charles L L. Brooks Iii posted to function by bilab on 2006-05-01 18:06:05 as along with 1 person oteri
	Hidden complexity of free energy surfaces for peptide (protein) folding. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 41. (12 October 2004), pp. 14766-14770. by S. V. Krivov, M. Karplus posted to folding by bilab on 2006-05-01 18:05:43 as along with 4 people apaydin dimka Diego_Prada Fernando_FF
	Folding of Ubiquitin: A Simple Model Describes the Strange Kinetics. [My Copy] J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 110, No. 17. (4 May 2006), pp. 8865-8869. by Sergei F. Chekmarev, Sergei V. Krivov, Martin Karplus posted to folding by bilab on 2006-05-01 17:59:19 as
	Molecular dynamics and protein function. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6679-6685. by M. Karplus, J. Kuriyan posted to function by bilab on 2006-05-01 17:57:50 as along with 5 people flbarroso onufriev apaydin allmensch RamuAnandakrishnan
	De novo protein design: towards fully automated sequence selection. [My Copy] J Mol Biol, Vol. 273, No. 4. (7 November 1997), pp. 789-796. by B. I. Dahiyat, C. A. Sarisky, S. L. Mayo posted to design by bilab on 2006-05-01 17:53:49 as
	Engineered antibody Fc variants with enhanced effector function. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 11. (14 March 2006), pp. 4005-4010. by G. A. Lazar, W. Dang, S. Karki, et al.O. Vafa, J. S. Peng, L. Hyun, C. Chan, H. S. Chung, A. Eivazi, S. C. Yoder, J. Vielmetter, D. F. Carmichael, R. J. Hayes, B. I. Dahiyat posted to function by bilab on 2006-05-01 17:44:41 as along with 1 person msuarezdiez
	The burial of solvent-accessible surface area is a predictor of polypeptide folding and misfolding as a function of chain elongation. [My Copy] J Am Chem Soc, Vol. 127, No. 45. (16 November 2005), pp. 15690-15691. by N. Kurt, S. Cavagnero posted to design by bilab on 2006-05-01 12:39:29 as along with 1 person hryk
	In quest of an empirical potential for protein structure prediction. [My Copy] Current opinion in structural biology, Vol. 16, No. 2. (6 April 2006), pp. 166-171. by J. Skolnick posted to prediction structure by bilab on 2006-05-01 12:36:18 as along with 4 people flbarroso krapnik BragilMassoud nigham
	Ensemble versus single-molecule protein unfolding. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 38. (20 September 2005), pp. 13445-13450. by R. Day, V. Daggett posted to folding by bilab on 2006-05-01 12:34:46 as along with 2 people choonpeng hmk
	The present view of the mechanism of protein folding. [My Copy] Nat Rev Mol Cell Biol, Vol. 4, No. 6. (June 2003), pp. 497-502. by V. Daggett, A. Fersht posted to folding by bilab on 2006-05-01 12:33:18 as along with 3 people and 2 groups ana okarsligil mirzazadeh structural_bioinformatics Bioinformatics
	Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates. [My Copy] Biophys J (14 April 2006) by Christopher D D. Snow, Young Min M. Rhee, Vijay S S. Pande posted to folding by bilab on 2006-05-01 12:29:36 as along with 1 person allmensch
	Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 14. (4 April 2006), pp. 5367-5372. by N. Koga, S. Takada posted to folding by bilab on 2006-05-01 12:26:34 as along with 1 person choonpeng
	Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent. [My Copy] Biophys J, Vol. 88, No. 5. (May 2005), pp. 3180-3190. by Y. Sugita, Y. Okamoto posted to folding by bilab on 2006-05-01 12:24:08 as along with 2 people jvf666 rulix
	Protonation of the acidic residues in the transmembrane cation-binding sites of the ca(2+) pump. [My Copy] J Am Chem Soc, Vol. 127, No. 17. (4 May 2005), pp. 6150-6151. by Y. Sugita, N. Miyashita, M. Ikeguchi, A. Kidera, C. Toyoshima posted to function by bilab on 2006-05-01 12:22:36 as
	Atomically detailed description of the unfolding of alpha-lactalbumin by the combined use of experiments and simulations. [My Copy] J Mol Biol, Vol. 354, No. 1. (18 November 2005), pp. 164-172. by T. Oroguchi, M. Ikeguchi, K. Saeki, et al.K. Kamagata, Y. Sawano, M. Tanokura, A. Kidera, K. Kuwajima posted to folding by bilab on 2006-05-01 12:20:37 as along with 1 person choonpeng
	Native protein sequences are designed to destabilize folding intermediates. [My Copy] Biochemistry, Vol. 45, No. 8. (28 February 2006), pp. 2488-2492. by Y. Isogai posted to design by bilab on 2006-05-01 12:18:31 as along with 1 person and 1 group nknii TCR_Signaling
	GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures. [My Copy] BMC Bioinformatics, Vol. 6 (2005) by D. M. Standley, H. Toh, H. Nakamura posted to algorithm by bilab on 2006-05-01 12:15:23 as along with 1 person and 1 group caporaso biomedical-nlp
	The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. [My Copy] Bioinformatics, Vol. 21, No. 17. (1 September 2005), pp. 3482-3489. by T. Sato, Y. Yamanishi, M. Kanehisa, H. Toh posted to evolution by bilab on 2006-05-01 12:14:27 as along with 2 people bioinfo cjeans
	The 3D profile method for identifying fibril-forming segments of proteins. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 11. (14 March 2006), pp. 4074-4078. by M. J. Thompson, S. A. Sievers, J. Karanicolas, M. I. Ivanova, D. Baker, D. Eisenberg posted to algorithm by bilab on 2006-05-01 12:13:52 as along with 2 people bobychan JIreland
	Atomic-level description of amyloid beta-dimer formation. [My Copy] J Am Chem Soc, Vol. 128, No. 7. (22 February 2006), pp. 2158-2159. by S. Gnanakaran, R. Nussinov, A. E. García posted to folding by bilab on 2006-05-01 12:11:11 as
	Simulating movement of tRNA into the ribosome during decoding. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 44. (1 November 2005), pp. 15854-15859. by K. Y. Sanbonmatsu, S. Joseph, C. S. Tung posted to function by bilab on 2006-05-01 12:09:47 as along with 2 people perrywoo ffranca
	Physically realistic homology models built with ROSETTA can be more accurate than their templates. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 14. (4 April 2006), pp. 5361-5366. by K. M. Misura, D. Chivian, C. A. Rohl, D. E. Kim, D. Baker posted to prediction structure by bilab on 2006-05-01 12:08:50 as along with 6 people kgutwin j3xucite jwm balajis dgront BioNica
	Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling [My Copy] Journal of Biomolecular NMR, Vol. 31, No. 1. (January 2005), pp. 59-64. by Jianhan Chen, Hyung-Sik Won, Wonpil Im, H. Dyson, Charles Brooks posted to refinement by bilab on 2006-05-01 12:05:55 as along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
	Refinement of NMR structures using implicit solvent and advanced sampling techniques. [My Copy] J Am Chem Soc, Vol. 126, No. 49. (15 December 2004), pp. 16038-16047. by J. Chen, W. Im, C. L. Brooks posted to refinement by bilab on 2006-05-01 12:04:57 as along with 2 people bmduggan baaden
	GROMACS: fast, flexible, and free. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1701-1718. by David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. Berendsen posted to software by bilab on 2006-05-01 12:03:19 as along with 20 people and 2 groups arifor krapnik r2s2 janneb dsmueller oteri choonpeng sebk dimka jwm ttjoseph rabio Dinler tji softsimu ashaytan robertvacha sunnytov Diego_Prada A_Coletta_Thesis Radiation_Damage Stressosome
	Molecular dynamics studies of the archaeal translocon. [My Copy] Biophys J (13 January 2006) by James C C. Gumbart, Klaus Schulten posted to function by bilab on 2006-05-01 12:02:32 as along with 1 person ruudvanleeuwen
	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 software by bilab on 2006-05-01 12:01:18 as along with 20 people and 5 groups krapnik pjkiley flbarroso yxue r2s2 grondina rpetrenko oteri oceanwind dfgreen vahmurk gisle dimka jwm ttjoseph sangeetha yoel_rf wilsoros sobolevnrm ibuch Radiation_Damage Stressosome Bioinformatics insilicodrug baker-group
	Folding Cooperativity in a Three-stranded beta-Sheet Model. [My Copy] J Mol Biol, Vol. 352, No. 2. (16 September 2005), pp. 370-381. by D. R. Roe, V. Hornak, C. Simmerling posted to folding by bilab on 2006-05-01 11:59:29 as along with 1 person fjc1
	A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase. [My Copy] Journal of medicinal chemistry, Vol. 49, No. 6. (23 March 2006), pp. 1837-1844. by Thomas Steinbrecher, David A. Case, Andreas Labahn posted to function by bilab on 2006-05-01 11:58:50 as along with 1 person bmduggan
	All-atom structure prediction and folding simulations of a stable protein. [My Copy] J Am Chem Soc, Vol. 124, No. 38. (25 September 2002), pp. 11258-11259. by C. Simmerling, B. Strockbine, A. E. Roitberg posted to folding by bilab on 2006-05-01 11:56:09 as along with 2 people fjc1 allmensch
	The Amber biomolecular simulation programs. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1668-1688. by David A. Case, Thomas E. Cheatham, Tom Darden, et al.Holger Gohlke, Ray Luo, Kenneth M. Merz, Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods posted to software by bilab on 2006-05-01 11:54:55 as along with 18 people and 3 groups krapnik csrocha nickolay mmuecke flbarroso charris5 pavanghatty tahereh62 lna jwm ttjoseph xdeupi tovrstra RamuAnandakrishnan IrinaMoreira adilson_mohr mikaellund gisle Radiation_Damage Stressosome LabCompMed
	Effective function annotation through catalytic residue conservation. [My Copy] Proc Natl Acad Sci U S A (21 July 2005) by Richard A A. George, Ruth V V. Spriggs, Gail J J. Bartlett, et al.Alex Gutteridge, Malcolm W W. Macarthur, Craig T T. Porter, Bissan Al-Lazikani, Janet M M. Thornton, Mark B B. Swindells posted to evolution by bilab on 2006-05-01 11:54:03 as along with 5 people and 1 group chrn Einat alexg gbart tny structural_bioinformatics
	An Analysis of Intron Positions in Relation to Nucleotides, Amino Acids, and Protein Secondary Structure. [My Copy] J Mol Biol (29 March 2006) by Gordon S S. Whamond, Janet M M. Thornton posted to evolution by bilab on 2006-05-01 11:52:55 as
	Ab initio molecular dynamics with discrete variable representation basis sets: techniques and application to liquid water. [My Copy] J Phys Chem A Mol Spectrosc Kinet Environ Gen Theory, Vol. 110, No. 16. (27 April 2006), pp. 5549-5560. by H. S. Lee, M. E. Tuckerman posted to algorithm by bilab on 2006-05-01 11:51:27 as
	Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain [j. Am. Chem. Soc. 2006, 128, 3019-3026]. [My Copy] J Am Chem Soc, Vol. 128, No. 13. (5 April 2006) by D. Zhang, J. Gillingsrud, J. A. McCammon posted to function by bilab on 2006-05-01 11:50:37 as
	Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models. [My Copy] Phys Rev Lett, Vol. 96, No. 8. (3 March 2006) by J. Dzubiella, J. M. Swanson, J. A. McCammon posted to algorithm by bilab on 2006-05-01 11:49:51 as
	Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids [My Copy] Biopolymers, Vol. 82, No. 2. (June 2006), pp. 106-120. by Robert Konecny, Joanna Trylska, Florence Tama, et al.Deqiang Zhang, Nathan A. Baker, Charles L. Brooks, J. A. McCammon posted to function by bilab on 2006-05-01 11:48:59 as along with 1 person RamuAnandakrishnan
	Balancing Solvation and Intramolecular Interactions: Toward a Consistent Generalized Born Force Field [My Copy] Journal of the American Chemical Society, Vol. 128, No. 11. (1 March 2006), pp. 3728-3736. by Jianhan Chen, Wonpil Im, Charles L. Brooks posted to algorithm by bilab on 2006-05-01 11:48:15 as along with 5 people ckmyo oteri yxue dfgreen onufriev