msuarezdiez's library 92 articles Export

	Analyzing Protein Interaction Networks Using Structural Information [My Copy] Annual Review of Biochemistry, Vol. 77, No. 1. (2008) by Christina Kiel, Pedro Beltrao, Luis Serrano posted to kiel2008 by msuarezdiez on 2009-06-12 11:47:18 as along with 11 people and 1 group flbarroso kshameer chad_davis Borelli bicko neils Evangelia grahamc paolomarcatili phoenixzxl zwang structural_bioinformatics
	Differentiation of regions with atypical oligonucleotide composition in bacterial genomes [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005) by Oleg Reva, Burkhard Tummler posted to oligonucleotide usage by msuarezdiez on 2009-03-24 15:29:36 as along with 1 person karfunkel
	Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (03 November 2008), 467. by Weijun Luo, Kurt Hankenson, Peter Woolf posted to microarray_data reverse_engineering by msuarezdiez on 2009-03-18 09:45:52 as along with 8 people sotacam kemalpak jfr pengchy lptolik druvus isimpson sjung
	Characterization of Two 2[4Fe4S] Ferredoxins from Clostridium acetobutylicum [My Copy] Current Microbiology, Vol. 56, No. 3. (7 March 2008), pp. 261-267. by Olivier Guerrini, Bénédicte Burlat, Christophe Léger, Bruno Guigliarelli, Philippe Soucaille, Laurence Girbal posted to ferredoxin hydrogenase by msuarezdiez on 2009-02-12 11:04:30 as
	Potential energy functions for protein design. [My Copy] Curr Opin Struct Biol (24 March 2007) by F Edward E. Boas, Pehr B B. Harbury posted to computational_protein_design by msuarezdiez on 2009-02-04 10:42:52 as along with 5 people kgutwin krapnik BragilMassoud aalibes onufriev
	Computational Design of Calmodulin Mutants with up to 900-Fold Increase in Binding Specificity. [My Copy] Journal of molecular biology (27 September 2008) by Eliyahu Yosef, Regina Politi, Mee H H. Choi, Julia M M. Shifman posted to computational_protein_design by msuarezdiez on 2009-02-03 16:18:39 as along with 2 people and 1 group higueruelo barry McCammon
	Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet Design [My Copy] Structure, Vol. 16, No. 12. (12 December 2008), pp. 1799-1805. by Xiaozhen Hu, Huanchen Wang, Hengming Ke, Brian Kuhlman posted to computational_protein_design by msuarezdiez on 2009-02-03 16:15:58 as along with 1 person jwm
	Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 1. (2 January 2007), pp. 48-53. by T. P. Treynor, C. L. Vizcarra, D. Nedelcu, S. L. Mayo posted to protein_design by msuarezdiez on 2009-01-13 15:31:31 as
	Crystal Structure of the Termination Module of a Nonribosomal Peptide Synthetase [My Copy] Science (26 June 2008), 1159850. by Alan Tanovic, Stefan A. Samel, Lars-Oliver Essen, Mohamed A. Marahiel posted to no-tag by msuarezdiez on 2009-01-13 14:53:23 as along with 1 person cychen_cite
	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 by msuarezdiez on 2009-01-07 16:46:24 as along with 6 people and 5 groups aqeel carlosjavierna apaydin barry joergkurtwegner LamBras structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data. [My Copy] Protein science : a publication of the Protein Society, Vol. 13, No. 2. (February 2004), pp. 549-554. by D. Zheng, J. M. Aramini, G. T. Montelione posted to protein_a by msuarezdiez on 2008-12-02 13:08:04 as
	Pareto optimization in computational protein design with multiple objectives [My Copy] Journal of Computational Chemistry, Vol. 29, No. 16. (2008), pp. 2704-2711. by María Suárez, Pablo Tortosa, Javier Carrera, Alfonso Jaramillo posted to computational_protein_design multipurpose by msuarezdiez on 2008-11-27 13:35:14 as
	Computer-aided design of modular protein devices: Boolean AND gene activation [My Copy] Phys. Biol., Vol. 3, No. 4. (December 2006), 295. by H. Salis, Y. N. Kaznessis posted to modular_proteins protein_design by msuarezdiez on 2008-11-25 14:11:28 as along with 1 person madhadron
	Atomic Resolution Modeling of the Ferredoxin:[FeFe] Hydrogenase Complex from Chlamydomonas reinhardtii [My Copy] Biophys. J. (27 July 2007), biophysj.107.108589. by Christopher H. Chang, Paul W. King, Maria L. Ghirardi, Kwiseon Kim posted to hydrogenase protein_design protein_docking by msuarezdiez on 2008-11-25 12:33:09 as
	High-resolution solution NMR structure of the Z domain of staphylococcal protein A [My Copy] Journal of Molecular Biology, Vol. 272, No. 4. (03 October 1997), pp. 573-590. by M. Tashiro posted to structural_biology x-ray by msuarezdiez on 2008-11-19 10:54:26 as
	A universal RNAi-based logic evaluator that operates in mammalian cells [My Copy] Nature Biotechnology, Vol. 25, No. 7. (21 May 2007), pp. 795-801. by Keller Rinaudo, Leonidas Bleris, Rohan Maddamsetti, Sairam Subramanian, Ron Weiss, Yaakov Benenson posted to rna rna_syntetic by msuarezdiez on 2008-11-06 12:55:48 as along with 3 people boko4ikameto guhjy stsaft
	RNA synthetic biology [My Copy] Nat Biotech, Vol. 24, No. 5. (05 May 2006), pp. 545-554. by Farren J. Isaacs, Daniel J. Dwyer, James J. Collins posted to rna_syntetic synthetic_biology by msuarezdiez on 2008-11-05 16:51:08 as along with 8 people and 4 groups abhishek_tiwari rklancer lingchong marcius balabu dbikard austin grahamc BioinfoCIPF SGU-CIPF Centre de Recherches Interdisciplinaires SynBioSys
	A modular and extensible RNA-based gene-regulatory platform for engineering cellular function [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 36. (4 September 2007), pp. 14283-14288. by Maung N. Win, Christina D. Smolke posted to hybridization rna by msuarezdiez on 2008-11-05 15:58:48 as along with 6 people and 2 groups cambray dchughes kengg zwang Jporci austin G4ID Genetics-of-Gambling
	Genetic parts to program bacteria. [My Copy] Curr Opin Biotechnol, Vol. 17, No. 5. (October 2006), pp. 548-557. by C. A. Voigt posted to synthetic_biology by msuarezdiez on 2008-10-23 16:46:55 as along with 3 people dswan jec105 austin
	Design of multi-specificity in protein interfaces. [My Copy] PLoS computational biology, Vol. 3, No. 8. (1 August 2007), e164. by Elisabeth L. Humphris, Tanja Kortemme posted to multipurpose protein_design by msuarezdiez on 2008-09-08 15:29:03 as along with 9 people and 3 groups bmduggan allmensch jwm bicko Einat dpollard Scis0000002 phoenixzxl marck structural_bioinformatics Bioinformatics EisenLab
	Computer-based redesign of a protein folding pathway [My Copy] Nat Struct Mol Biol, Vol. 8, No. 7. (July 2001), pp. 602-605. by Sehat Nauli, Brian Kuhlman, David Baker posted to nauli2001 by msuarezdiez on 2008-09-03 15:30:34 as
	Computational method to reduce the search space for directed protein evolution. [My Copy] Proc Natl Acad Sci U S A, Vol. 98, No. 7. (27 March 2001), pp. 3778-3783. by C. A. Voigt, S. L. Mayo, F. H. Arnold, Z. G. Wang posted to computational_protein_design by msuarezdiez on 2008-09-03 11:33:51 as along with 2 people and 1 group betainverse nknii TCR_Signaling
	Are database-derived potentials valid for scoring both forward and inverted protein folding? [My Copy] Protein Eng., Vol. 8, No. 9. (1 September 1995), pp. 849-858. by Marianne J. Rooman, Shoshana J. Wodak posted to protein_design by msuarezdiez on 2008-09-01 15:21:14 as
	Solvated docking: introducing water into the modelling of biomolecular complexes. [My Copy] Bioinformatics (9 August 2006) by Aalt D J D. van Dijk, Alexandre M J J M. Bonvin posted to protein_design protein_docking water by msuarezdiez on 2008-09-01 13:32:10 as along with 5 people and 1 group arlam BragilMassoud bicko jteyra Lombardo_7 Chang group
	Extending Iterative Protein Redesign and Optimization (IPRO) in Protein Library Design for Ligand Specificity [My Copy] Biophys. J., Vol. 92, No. 6. (15 March 2007), pp. 2120-2130. by Hossein Fazelinia, Patrick C. Cirino, Costas D. Maranas posted to optimization protein_design by msuarezdiez on 2008-07-23 09:39:07 as
	Energy Functions for Protein Design: Adjustment with Protein-Protein Complex Affinities, Models for the Unfolded State, and Negative Design of Solubility and Specificity [My Copy] Journal of Molecular Biology, Vol. 347, No. 1. (18 March 2005), pp. 203-227. by Navin Pokala, Tracy M. Handel posted to protein_design by msuarezdiez on 2008-07-22 12:56:58 as
	Design of a Hyperstable Protein by Rational Consideration of Unfolded State Interactions [My Copy] J. Am. Chem. Soc., Vol. 128, No. 10. (15 March 2006), pp. 3144-3145. by B. Anil, R. Craig-Schapiro, D. P. Raleigh posted to protein_design unfolded_state by msuarezdiez on 2008-07-22 10:25:41 as
	Role of residual structure in the unfolded state of a thermophilic protein. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 20. (30 September 2003), pp. 11345-11349. by Srebrenka Robic, Mercedes Guzman-Casado, Jose M. Sanchez-Ruiz, Susan Marqusee posted to protein_design unfolded_state by msuarezdiez on 2008-07-22 10:09:46 as along with 2 people min013 choonpeng
	Acceptable Protein and Solvent Behavior in Primary Hydration Shell Simulations of Hen Lysozyme [My Copy] Biophys. J., Vol. 92, No. 7. (1 April 2007), pp. L49-51. by Mehdi B. Hamaneh, Matthias Buck posted to implicit solvation by msuarezdiez on 2008-07-21 13:33:40 as along with 2 people allmensch saravan
	A ?solvated rotamer? approach to modeling water-mediated hydrogen bonds at protein-protein interfaces [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 58, No. 4. (2005), pp. 893-904. by Lin Jiang, Brian Kuhlman, Tanja Kortemme, David Baker posted to solvent by msuarezdiez on 2008-07-15 17:22:26 as along with 4 people oceanwind apaydin jwm skoddet
	Explicit and implicit water simulations of a &bgr;-hairpin peptide [My Copy] Proteins: Structure, Function, and Genetics, Vol. 37, No. 1. (1999), pp. 73-87. by Buyong Ma, Ruth Nussinov posted to ma1999 by msuarezdiez on 2008-07-15 17:01:45 as
	Free energy landscape of protein folding in water: Explicit vs. implicit solvent [My Copy] Proteins: Structure, Function, and Genetics, Vol. 53, No. 2. (2003), pp. 148-161. by Ruhong Zhou posted to explicit_solvent by msuarezdiez on 2008-07-15 16:58:33 as along with 5 people chemrahul82 flbarroso choonpeng RamuAnandakrishnan onufriev
	Protein Folding in the Absence of the Solvent Ordering Contribution to the Hydrophobic Interaction [My Copy] Journal of Molecular Biology, Vol. 229, No. 2. (20 January 1993), pp. 502-511. by Derek N. Woolfson, Alan Cooper, Margaret M. Harding, Dudley H. Williams, Philip A. Evans posted to protein_design solvent by msuarezdiez on 2008-07-15 16:07:48 as
	Toward Full-Sequence De Novo Protein Design with Flexible Templates for Human Beta-Defensin-2 [My Copy] Biophys. J., Vol. 94, No. 2. (15 January 2008), pp. 584-599. by Ho K. Fung, Christodoulos A. Floudas, Martin S. Taylor, Li Zhang, Dimitrios Morikis posted to protein_design by msuarezdiez on 2008-07-08 10:54:40 as
	Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences. [My Copy] Proteins, Vol. 62, No. 3. (15 March 2006), pp. 739-748. by X. Hu, B. Kuhlman posted to protein_design by msuarezdiez on 2008-06-25 15:14:47 as along with 3 people Lombardo_7 apaydin cat_worth
	De Novo Protein Design. I. In Search of Stability and Specificity [My Copy] Journal of Molecular Biology (November 1999), pp. 1161-1181. by P. Koehl, M. Levitt posted to protein_design by msuarezdiez on 2008-06-19 11:43:00 as
	Energy estimation in protein design [My Copy] Current Opinion in Structural Biology, Vol. 12, No. 4. (1 August 2002), pp. 441-446. by Joaquim Mendes, Raphael Guerois, Luis Serrano posted to protein_design by msuarezdiez on 2008-06-19 10:39:22 as
	Computational protein design [My Copy] Current Opinion in Chemical Biology, Vol. 5, No. 6. (1 December 2001), pp. 690-695. by Christina M. Kraemer-Pecore, Andrew M. Wollacott, John R. Desjarlais posted to protein_design by msuarezdiez on 2008-06-19 10:31:10 as
	Determination of the recognition sites of cytosine DNA-methylases from Escherichia coli SK [My Copy] Nucl. Acids Res., Vol. 7, No. 2. (25 September 1979), pp. 517-528. by I. I. Nikolskaya, N. G. Lopatina, N. V. Anikeicheva, S. S. Debov posted to methylation by msuarezdiez on 2008-06-06 10:29:09 as
	CpG Methylation Modifies the Genetic Stability of Cloned Repeat Sequences [My Copy] Genome Res., Vol. 12, No. 8. (1 August 2002), pp. 1246-1256. by Kerrie Nichol, And C. Pearson posted to methylation by msuarezdiez on 2008-06-06 10:23:12 as
	Hemimethylation prevents DNA replication in E. coli [My Copy] Cell, Vol. 50, No. 7. (25 September 1987), pp. 1071-1079. by David W. Russell, Norton D. Zinder posted to methylation by msuarezdiez on 2008-06-06 10:05:26 as
	Genome-wide prediction of G4 DNA as regulatory motifs: Role in Escherichia coli global regulation [My Copy] Genome Res., Vol. 16, No. 5. (1 May 2006), pp. 644-655. by Pooja Rawal, Veera B. Kummarasetti, Jinoy Ravindran, et al.Nirmal Kumar, Kangkan Halder, Rakesh Sharma, Mitali Mukerji, Swapan K. Das, Shantanu Chowdhury posted to varios by msuarezdiez on 2008-06-05 16:43:12 as along with 1 person supercoiling
	Anatomy of Escherichia coli sigma70 promoters. [My Copy] Nucleic Acids Res (22 December 2006) by Ryan K K. Shultzaberger, Zehua Chen, Karen A A. Lewis, Thomas D D. Schneider posted to promoter by msuarezdiez on 2008-06-05 09:53:27 as along with 1 person aswin
	Activities of Constitutive Promoters in Escherichia coli [My Copy] Journal of Molecular Biology (September 1999), pp. 19-37. by S. T. Liang, M. Bipatnath, Y. C. Xu, et al.S. L. Chen, P. Dennis, M. Ehrenberg, H. Bremer posted to promoter by msuarezdiez on 2008-06-04 12:53:51 as
	Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. [My Copy] Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007) by J. D. Sander, P. Zaback, J. K. Joung, D. F. Voytas, D. Dobbs posted to zinc_fingers by msuarezdiez on 2008-05-22 10:51:03 as along with 2 people guhjy austin
	Function of the zinc finger in Escherichia coli Fpg protein [My Copy] J. Biol. Chem., Vol. 268, No. 35. (15 December 1993), pp. 26738-26744. by J. Tchou, M. L. Michaels, J. H. Miller, A. P. Grollman posted to zinc_fingers_ecoli by msuarezdiez on 2008-05-19 15:43:35 as along with 1 person ramiro2k
	DksA affects ppGpp induction of RpoS at a translational level. [My Copy] J Bacteriol, Vol. 184, No. 16. (August 2002), pp. 4455-4465. by L. Brown, D. Gentry, T. Elliott, M. Cashel posted to zinc_fingers by msuarezdiez on 2008-05-19 15:38:59 as along with 1 person beny
	A comprehensive library of fluorescent transcriptional reporters for Escherichia coli [My Copy] Nature Methods, Vol. 3, No. 8. (21 July 2006), pp. 623-628. by Alon Zaslaver, Anat Bren, Michal Ronen, et al.Shalev Itzkovitz, Ilya Kikoin, Seagull Shavit, Wolfram Liebermeister, Michael G. Surette, Uri Alon posted to zinc_fingers by msuarezdiez on 2008-05-19 15:17:08 as
	Zinc-finger motifs expressed in E. coli and folded in vitro direct specific binding to DNA [My Copy] Nature, Vol. 332, No. 6161. (17 March 1988), pp. 284-286. by Kiyoshi Nagai, Yukinobu Nakaseko, Kim Nasmyth, Daniela Rhodes posted to zinc_fingers by msuarezdiez on 2008-05-19 14:40:01 as
	Insights into the molecular recognition of the 5'-GNN-3' family of DNA sequences by zinc finger domains [My Copy] Journal of Molecular Biology, Vol. 303, No. 4. (3 November 2000), pp. 489-502. by Birgit Dreier, David J. Segal, Carlos F. Barbas posted to zinc_fingers by msuarezdiez on 2008-05-15 10:45:51 as

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protein_design	18
computational_protein_design	12
protein	8
zinc_fingers	7
computational	6
design	6
promiscuity	6
enzyme	5
enzyme_design	5
operon	5
dynamics	4
molecular	4
prediction	4
charmm	3
methylation	3
multipurpose	3
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bioinformatics	2
evolvability	2
ezyme	2
hydrogenase	2
implicit	2
protein_docking	2
rna	2
rna_syntetic	2
structural	2
synthetic_biology	2
unfolded_state	2
biology	1
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biosensor	1
computationalprotein	1
d-aminoacids	1
desig	1
desing	1
enantiomers	1
explicit_solvent	1
ferredoxin	1
hybridization	1
kiel2008	1
ma1999	1
microarray_data	1
modular_proteins	1
monte-carlo	1
nauli2001	1
oligonucleotide	1
opinion	1
optimization	1
predcition	1
promoter_library	1
protein_a	1
prueba	1
reverse_engineering	1
review	1
solvation	1
structural_biology	1
transcriptional-terminators	1
usage	1
varios	1
water	1
x-ray	1
zinc_fingers_ecoli	1

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