Group: structural_bioinformatics - with tag protein_design [45 articles] Export

Recent papers posted by members of the structural_bioinformatics group with tag protein_design

	Rational stabilization of enzymes by computational redesign of surface charge-charge interactions. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (5 February 2009) by Alexey V V. Gribenko, Mayank M M. Patel, Jiajing Liu, Scott A A. McCallum, Chunyu Wang, George I I. Makhatadze posted to protein_design by barry to the group structural_bioinformatics on 2009-02-09 06:41:14 as along with 3 people and 2 groups sobolevnrm grahamc amishp baker-group McCammon
	Surface Sites for Engineering Allosteric Control in Proteins [My Copy] Science, Vol. 322, No. 5900. (17 October 2008), pp. 438-442. by Jeeyeon Lee, Madhusudan Natarajan, Vishal C. Nashine, et al.Michael Socolich, Tina Vo, William P. Russ, Stephen J. Benkovic, Rama Ranganathan posted to allosteric correlated_mutations protein_design sca by barry to the group structural_bioinformatics on 2008-10-17 03:06:04 as along with 7 people and 3 groups sobolevnrm jbhiatt lflorez cactus marck i000 paulschlesinger baker-group McCammon Bioinformatics
	Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (30 September 2008) by Mohammad Monirul M. Islam, Shihori Sohya, Keiichi Noguchi, Masafumi Yohda, Yutaka Kuroda posted to bpti protein_design protein_structure by barry to the group structural_bioinformatics on 2008-10-05 19:12:36 as along with 2 groups McCammon Bioinformatics
	De Novo Computational Design of Retro-Aldol Enzymes [My Copy] Science, Vol. 319, No. 5868. (7 March 2008), pp. 1387-1391. by Lin Jiang, Eric A. Althoff, Fernando R. Clemente, et al.Lindsey Doyle, Daniela Rothlisberger, Alexandre Zanghellini, Jasmine L. Gallaher, Jamie L. Betker, Fujie Tanaka, Carlos F. Barbas, Donald Hilvert, Kendall N. Houk, Barry L. Stoddard, David Baker posted to protein_design protein_ligand structure_refinement by barry to the group structural_bioinformatics on 2008-03-20 00:05:53 as along with 17 people and 3 groups barmak7282 baiaixi fralium qbin1304 alexknight aalibes jwm aprasad dgront zwang sobolevnrm davidlott msuarezdiez scienbox ucbcjbm joseph_x_zhou cambray Biocatalysis and Biotransformation baker-group McCammon
	Supercharging Proteins Can Impart Unusual Resilience [My Copy] J. Am. Chem. Soc., Vol. 129, No. 33. (22 August 2007), pp. 10110-10112. by M. S. Lawrence, K. J. Phillips, D. R. Liu posted to electrostatics journal_club protein_design protein_evolution protein_folding by barry to the group structural_bioinformatics on 2007-10-26 22:37:58 as along with 2 people and 2 groups samjlord sobolevnrm moernerlab baker-group
	Computational Design of a Single Amino Acid Sequence that Can Switch between Two Distinct Protein Folds. [My Copy] J Am Chem Soc, Vol. 128, No. 4. (1 February 2006), pp. 1154-1161. by X. I. Ambroggio, B. Kuhlman posted to protein_structure protein_sequence protein_dynamics protein_design by barry to the group structural_bioinformatics on 2007-09-04 19:32:05 as along with 5 people and 1 group shuns jwm kevinchannon bethbromley ca3295 Bioinformatics
	Optimization of specificity in a cellular protein interaction network by negative selection. [My Copy] Nature, Vol. 426, No. 6967. (11 December 2003), pp. 676-680. by A. Zarrinpar, S. H. Park, W. A. Lim posted to protein_structure protein_sequence protein_protein protein_evolution protein_design by barry to the group structural_bioinformatics on 2007-09-04 19:25:04 as along with 4 people and 1 group grahamc cjeans paolomarcatili phoenixzxl Bioinformatics
	Evolution of Function in the "Two Dinucleotide Binding Domains" Flavoproteins [My Copy] PLoS Comput Biol, Vol. 3, No. 7. (20 July 2007), e121. by Sunil Ojha, Elaine C. Meng, Patricia C. Babbitt posted to protein_structure protein_evolution protein_design fad by barry to the group structural_bioinformatics on 2007-07-20 18:33:27 as along with 5 people and 1 group anuragsethi pradiptaray Einat zwang mdimon Bioinformatics
	Principles determining the structure of [beta]-sheet barrels in proteins II. The observed structures [My Copy] Journal of Molecular Biology, Vol. 236, No. 5. (11 March 1994), pp. 1382-1400. by Alexey G. Murzin, Arthur M. Lesk, Cyrus Chothia posted to protein_structure protein_packing protein_design beta_sheet by barry to the group structural_bioinformatics on 2007-01-18 19:23:39 as along with 1 group Bioinformatics
	Principles determining the structure of [beta]-sheet barrels in proteins I. A theoretical analysis [My Copy] Journal of Molecular Biology, Vol. 236, No. 5. (11 March 1994), pp. 1369-1381. by Alexey G. Murzin, Arthur M. Lesk, Cyrus Chothia posted to protein_structure protein_packing protein_design beta_sheet by barry to the group structural_bioinformatics on 2007-01-18 19:21:40 as along with 1 group Bioinformatics
	Fluctuations in ion pairs and their stabilities in proteins. [My Copy] Proteins, Vol. 43, No. 4. (1 June 2001), pp. 433-454. by S. Kumar, R. Nussinov posted to ion_pairs protein_design protein_structure by barry to the group structural_bioinformatics on 2006-10-26 01:03:28 as along with 1 group Bioinformatics
	Relationship between ion pair geometries and electrostatic strengths in proteins. [My Copy] Biophys J, Vol. 83, No. 3. (September 2002), pp. 1595-1612. by S. Kumar, R. Nussinov posted to ion_pairs protein_design protein_structure by barry to the group structural_bioinformatics on 2006-10-26 01:01:29 as along with 1 person and 1 group bicko Bioinformatics
	Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering [My Copy] Proteins, Vol. 65, No. 2. (1 November 2006), pp. 463-479. by Jiang Zhu, Li Xie, Barry Honig posted to protein_design protein_fragments protein_structure by barry to the group structural_bioinformatics on 2006-10-10 01:34:49 as along with 1 group Bioinformatics
	Protein flexibility acclimatizes photosynthetic energy conversion to the ambient temperature [My Copy] Nature, Vol. 442, No. 7104. (23 July 2006), pp. 827-830. by Oksana Shlyk-Kerner, Ilan Samish, David Kaftan, et al.Neta Holland, Maruthi P. S. Sai, Hadar Kless, Avigdor Scherz posted to domain_motions protein_design protein_dynamics protein_structure by barry to the group structural_bioinformatics on 2006-08-16 21:45:51 as along with 1 group Bioinformatics
	Structural diversity of domain superfamilies in the CATH database. [My Copy] Journal of molecular biology, Vol. 360, No. 3. (14 July 2006), pp. 725-741. by Gabrielle A. Reeves, Timothy J. Dallman, Oliver C. Redfern, Adrian Akpor, Christine A. Orengo posted to cath protein_design protein_evolution protein_protein protein_structure by barry to the group structural_bioinformatics on 2006-07-07 19:57:04 as along with 4 people and 4 groups martainn yuslinaz marcius sobolevnrm Bioinformatics BioinfoCIPF SGU-CIPF baker-group
	Composites of local structure propensities: evidence for local encoding of long-range structure [My Copy] Protein Science: a Publication Of The Protein Society, Vol. 11, No. 1. (January 2002), pp. 18-26. by David Shortle posted to protein_design protein_structure by barry to the group structural_bioinformatics on 2006-04-10 19:44:48 as along with 1 person and 1 group Einat Bioinformatics
	A physical basis for protein secondary structure [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 25. (1999), pp. 14258-14263. by R. Srinivasan, G. D. Rose posted to protein_design protein_structure by barry to the group structural_bioinformatics on 2006-04-10 19:43:36 as along with 1 person and 1 group Einat Bioinformatics
	Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns [My Copy] Protein Science: a Publication Of The Protein Society, Vol. 6, No. 7. (July 1997), pp. 1587-1590. by K. F. Han, C. Bystroff, D. Baker posted to protein_design protein_structure by barry to the group structural_bioinformatics on 2006-04-10 19:41:42 as along with 1 group Bioinformatics
	Rotamer Libraries in the 21st Century [My Copy] Current Opinion in Structural Biology, Vol. 12, No. 4. (1 August 2002), pp. 431-440. by R. Dunbrack posted to protein_design protein_dynamics protein_structure by barry to the group structural_bioinformatics on 2006-04-10 19:39:07 as along with 6 people and 4 groups aqeel msuarezdiez carlosjavierna apaydin joergkurtwegner LamBras Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	The penultimate rotamer library [My Copy] Proteins, Vol. 40, No. 3. (15 August 2000), pp. 389-408. by S. C. Lovell, J. M. Word, J. S. Richardson, D. C. Richardson posted to protein_design protein_dynamics protein_structure by barry to the group structural_bioinformatics on 2006-04-10 19:37:07 as along with 3 people and 4 groups csrocha joergkurtwegner LamBras Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	Structure validation by Calpha geometry: phi,psi and Cbeta deviation [My Copy] Proteins, Vol. 50, No. 3. (15 February 2003), pp. 437-450. by Simon C. Lovell, Ian W. Davis, Arendall, et al.Paul I. de Bakker, Michael J. Word, Michael G. Prisant, Jane S. Richardson, David C. Richardson posted to protein_design protein_structure by barry to the group structural_bioinformatics on 2006-04-10 19:34:42 as along with 3 people and 5 groups mikelape sangeetha joergkurtwegner Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
	Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms1 [My Copy] Journal of Molecular Biology, Vol. 285, No. 4. (29 January 1999), pp. 1711-1733. by Word, Simon C. Lovell, Thomas H. Labean, et al.Hope C. Taylor, Michael E. Zalis, Brent K. Presley, Jane S. Richardson, David C. Richardson posted to protein_design protein_structure by barry to the group structural_bioinformatics on 2006-04-10 19:27:22 as along with 4 people and 4 groups Diego_Prada aqeel dgront joergkurtwegner Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins [My Copy] Science, Vol. 312, No. 5770. (7 April 2006), pp. 111-114. by Daniel M. Weinreich, Nigel F. Delaney, Mark A. Depristo, Daniel L. Hartl posted to protein_design protein_evolution protein_sequence by barry to the group structural_bioinformatics on 2006-04-07 20:25:19 as along with 14 people and 4 groups stevanspringer pansapiens imouthesmp dayjm Einat marcius i41m nirfriedman cmm RowanBarrett ramensky Vaquero Ema bpcusack Bioinformatics FAB-lab BioinfoCIPF SGU-CIPF
	Some fundamental aspects of building protein structures from fragment libraries. [My Copy] Protein Sci, Vol. 13, No. 6. (June 2004), pp. 1636-1650. by J. B. Holmes, J. Tsai posted to protein_design protein_fragments by barry to the group structural_bioinformatics on 2006-03-22 20:21:32 as along with 2 people and 1 group eckart_bindewald wouterboomsma Bioinformatics
	Folding free energy function selects native-like protein sequences in the core but not on the surface [My Copy] PNAS, Vol. 99, No. 21. (15 October 2002), pp. 13554-13559. by Alfonso Jaramillo, Lorenz Wernisch, Stephanie Hery, Shoshana J. Wodak posted to protein_design protein_structure by barry to the group structural_bioinformatics on 2006-03-22 20:18:42 as along with 1 group Bioinformatics
	Clustering of low-energy conformations near the native structures of small proteins. [My Copy] Proc Natl Acad Sci U S A, Vol. 95, No. 19. (15 September 1998), pp. 11158-11162. by D. Shortle, K. T. Simons, D. Baker posted to protein_design protein_dynamics protein_folding protein_sequence protein_structure by barry to the group structural_bioinformatics on 2006-03-22 20:15:18 as along with 3 people and 4 groups thaliana dgront joergkurtwegner Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. [My Copy] J Mol Biol, Vol. 307, No. 5. (13 April 2001), pp. 1487-1502. by R. Landgraf, I. Xenarios, D. Eisenberg posted to protein_design protein_protein protein_sequence protein_structure residue_annotation by barry to the group structural_bioinformatics on 2006-03-02 22:37:16 as along with 8 people and 1 group dfdong ramiro2k pansapiens sriram_s cjeans mingzhi Pao-Yang marti Bioinformatics
	Allosteric Regulation of Hsp70 Chaperones by a Proline Switch [My Copy] Molecular Cell, Vol. 21, No. 3. (3 February 2006), pp. 359-367. by Markus Vogel, Bernd Bukau, Matthias P. Mayer posted to allosteric hsp70 protein_design protein_dynamics protein_structure by barry to the group structural_bioinformatics on 2006-02-03 02:52:39 as along with 1 person and 2 groups pdelosri Bioinformatics EPFL_SB_ITP_LBS
	Ran's C-terminal, basic patch, and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras, and Ran GTPases. [My Copy] Genome Res, Vol. 13, No. 4. (April 2003), pp. 673-692. by A. F. Neuwald, N. Kannan, A. Poleksic, N. Hata, J. S. Liu posted to allosteric bioinf_methods contacts core_residues g_proteins ntpases p-loop protein_design protein_dynamics protein_evolution protein_sequence protein_structure by barry to the group structural_bioinformatics on 2006-01-07 03:57:13 as along with 1 group Bioinformatics
	Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity. [My Copy] Proteins, Vol. 37, No. 3. (15 November 1999), pp. 379-387. by N. Blomberg, R. R. Gabdoulline, M. Nilges, R. C. Wade posted to electrostatics protein_design protein_sequence protein_structure by barry to the group structural_bioinformatics on 2005-10-10 09:29:59 as along with 1 group Bioinformatics
	Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. [My Copy] Proteins, Vol. 30, No. 2. (1 February 1998), pp. 144-154. by S. Hayward, H. J. Berendsen posted to bioinf_methods domain_motions protein_design protein_dynamics protein_structure by barry to the group structural_bioinformatics on 2005-10-09 08:22:02 as along with 1 group Bioinformatics
	Conservation of electrostatic properties within enzyme families and superfamilies. [My Copy] Biochemistry, Vol. 42, No. 12. (1 April 2003), pp. 3464-3473. by D. R. Livesay, P. Jambeck, A. Rojnuckarin, S. Subramaniam posted to electrostatics protein_design protein_evolution protein_structure by barry to the group structural_bioinformatics on 2005-10-09 01:28:18 as along with 1 person and 1 group Einat Bioinformatics
	Automatic Analysis of Protein Conformational Changes by Multiple Linkage Clustering [My Copy] Journal of Molecular Biology, Vol. 253, No. 4. (3 November 1995), pp. 633-647. by Nathalie S. Boutonnet, Marianne J. Rooman, Shoshana J. Wodak posted to bioinf_methods protein_design protein_dynamics protein_structure by barry to the group structural_bioinformatics on 2005-09-28 01:16:22 as along with 1 group Bioinformatics
	Structural biologyForm and function instructions [My Copy] Nature, Vol. 437, No. 7058. (21 September 2005), pp. 486-487. by Jeffery W. Kelly posted to correlated_mutations protein_design protein_sequence protein_structure statistical_coupling_analysis by ana to the group structural_bioinformatics on 2005-09-22 23:01:12 as along with 2 people and 1 group barry dayjm Bioinformatics
	Natural-like function in artificial WW domains [My Copy] Nature, Vol. 437, No. 7058., pp. 579-583. by William P. Russ, Drew M. Lowery, Prashant Mishra, Michael B. Yaffe, Rama Ranganathan posted to correlated_mutations protein_design protein_sequence protein_structure statistical_coupling_analysis by ana to the group structural_bioinformatics on 2005-09-22 23:00:20 as along with 6 people and 4 groups barry balajis marcius caporaso bethbromley ca3295 Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
	Identifying and engineering ion pairs in adenylate kinases. Insights from molecular dynamics simulations of thermophilic and mesophilic homologues [My Copy] The Journal Of Biological Chemistry, Vol. 280, No. 35. (2 September 2005), pp. 30943-30948. by Euiyoung Bae, George N. Phillips posted to ion_pairs kinases md_simulation protein_design by barry to the group structural_bioinformatics on 2005-09-20 18:56:31 as along with 1 group Bioinformatics
	Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding. [My Copy] Protein Sci, Vol. 3, No. 5. (May 1994), pp. 769-778. by D. Fischer, H. Wolfson, S. L. Lin, R. Nussinov posted to bioinf_methods protein_design protein_evolution protein_structure structural_bioinformatics structure_comparison by barry to the group structural_bioinformatics on 2005-09-19 22:03:37 as along with 4 people and 1 group aalibes shadowman tjimenez chrys Bioinformatics
	A method to predict functional residues in proteins. [My Copy] Nat Struct Biol, Vol. 2, No. 2. (February 1995), pp. 171-178. by G. Casari, C. Sander, A. Valencia posted to bioinf_methods correlated_mutations protein_design protein_sequence sequence_comparison by barry to the group structural_bioinformatics on 2005-09-16 23:37:03 as along with 2 people and 1 group ramiro2k sriram_s Bioinformatics
	In silico Discovery of Enzyme-Substrate Specificity-determining Residue Clusters [My Copy] Journal of Molecular Biology, Vol. 352, No. 5. (7 October 2005), pp. 1105-1117. by Gong-Xin Yu, Byung-Hoon Park, Praveen Chandramohan, Rajesh Munavalli, Al Geist, Nagiza F. Samatova posted to bioinf_methods correlated_mutations protein_design protein_evolution protein_sequence sequence_comparison by barry to the group structural_bioinformatics on 2005-09-15 18:06:44 as along with 1 person and 1 group cjeans Bioinformatics
	Small Libraries of Protein Fragments Model Native Protein Structures Accurately [My Copy] Journal of Molecular Biology, Vol. 323, No. 2. (18 October 2002), pp. 297-307. by Rachel Kolodny, Patrice Koehl, Leonidas Guibas, Michael Levitt posted to comparative_model protein_design protein_evolution protein_structure structural_bioinformatics structure_comparison by barry to the group structural_bioinformatics on 2005-09-07 17:59:27 as along with 1 group Bioinformatics
	Small libraries of protein fragments model native protein structures accurately. [My Copy] J Mol Biol, Vol. 323, No. 2. (18 October 2002), pp. 297-307. by R. Kolodny, P. Koehl, L. Guibas, M. Levitt posted to comparative_modeling protein_design protein_evolution protein_structure structure_comparison structure_fragments by ana to the group structural_bioinformatics on 2005-09-07 17:58:32 as along with 3 people and 1 group barry eckart_bindewald j3xucite Bioinformatics
	Identification of functionally conserved residues with the use of entropy-variability plots. [My Copy] Proteins, Vol. 52, No. 4. (1 September 2003), pp. 544-552. by L. Oliveira, P. B. Paiva, A. C. Paiva, G. Vriend posted to bioinformatics protein_design protein_sequence sequence_comparison by barry to the group structural_bioinformatics on 2005-08-01 22:41:32 as along with 1 group Bioinformatics
	PKA: a portrait of protein kinase dynamics [My Copy] Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, Vol. 1697, No. 1-2. (11 March 2004), pp. 259-269. by S. Taylor, J. Yang, J. Wu, N. Haste, E. Radzio-Andzelm, G. Anand posted to kinases protein_design review by barry to the group structural_bioinformatics on 2005-05-25 00:01:55 as along with 1 person and 1 group neils Bioinformatics
	Recapitulation of protein family divergence using flexible backbone protein design. [My Copy] J Mol Biol, Vol. 346, No. 2. (18 February 2005), pp. 631-644. by C. T. Saunders, D. Baker posted to protein_design structure_comparison structure_flexible by ana to the group structural_bioinformatics on 2005-05-11 19:13:26 as along with 1 person and 1 group barry Bioinformatics
	STRUCTURAL BIOLOGY: Learning to Speak the Language of Proteins [My Copy] Science, Vol. 302, No. 5649. (21 November 2003), pp. 1347-1348. by David T. Jones posted to protein_design protein_folding protein_structure sequence_structure by ana to the group structural_bioinformatics on 2005-05-06 21:50:01 as along with 1 person and 1 group karbak Bioinformatics

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protein_structure	139
crystallization	43
protein_sequence	41
protein_evolution	38
protein_dynamics	35
bioinf_methods	22
correlated_mutations	21
protein_folding	20
structure_comparison	16
ankyrin	15
rosetta	15
data	13
protein_protein	11
allosteric	10
protein_engineering	10
sequence_comparison	10
structural_bioinformatics	10
alternatives	9
de_novo_protein	9
ion_pairs	9
mn	9
electrostatics	8
nonviral_gene_delivery	8
protein_fragments	8
review	8
membrane2soluble	7
protein_packing	7
beta_sheet	6
comparative_model	6
core_residues	6
domain_motions	6
kinases	6
statistical_coupling_analysis	6
contacts	5
negative_design	5
scp	5
artificial_photosynthesis	4
bioinformatics	4
bpti	4
core_structure	4
entropy	4
protein	4
protein_ligand	4
protein_ligand_binding	4
rotamer_libraries	4
sca	4
structure_refinement	4
beta_propeller	3
bioengineering	3
cath	3
comparative_modeling	3
fad	3
ferritin	3
free_energy	3
g_proteins	3
hsp70	3
hydrogenase	3
md_simulation	3
metalloenzyme	3
mn_enzyme	3
molecular_mechanics	3
nanoparticle	3
ntpases	3
p-loop	3
protein_stability	3
psii	3
residue_annotation	3
rotamer	3
sequence_structure	3
structure_flexible	3
structure_fragments	3
synthetic_biology	3
tesis	3
13-nov-09	2
amin_acids	2
aminoacid_substitution	2
backrub	2
beta_solenoid	2
coiled_coil	2
egad	2
experimental	2
helix_helix	2
journal_club	2
nrps	2
peptide_self_assembly	2
protein-design	2
protein-prediction	2
protein-sequence-design	2
protein_docking	2
protein_protein_interactions	2
proteins	2
reaction_centre	2
reation_centre	2
side_chain_flexibility	2
specificity	2
statistical_physics	2
structure_aided	2
thesis	2
viruses	2
web_tool	2

Group: structural_bioinformatics - with tag protein_design [45 articles] Export

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