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msuarezdiez's library [68 articles]

Recent papers added to msuarezdiez's library.
  • Extending Iterative Protein Redesign and Optimization (IPRO) in Protein Library Design for Ligand Specificity
    Biophys. J., Vol. 92, No. 6. (15 March 2007), pp. 2120-2130.
    by Hossein Fazelinia, Patrick C Cirino, Costas D Maranas
    posted to protein_design optimization 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
    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
    J. Am. Chem. Soc., Vol. 128, No. 10. (15 March 2006), pp. 3144-3145.
    by B Anil, R Craig-Schapiro, DP Raleigh
    posted to unfolded_state protein_design by msuarezdiez on 2008-07-22 10:25:41 as **
  • Role of residual structure in the unfolded state of a thermophilic protein.
    Proc Natl Acad Sci U S A, Vol. 100, No. 20. (30 September 2003), pp. 11345-11349.
    by S Robic, M Guzman-Casado, JM Sanchez-Ruiz, S Marqusee
    posted to unfolded_state protein_design by msuarezdiez on 2008-07-22 10:09:46 as ** along with 1 person choonpeng
  • Acceptable Protein and Solvent Behavior in Primary Hydration Shell Simulations of Hen Lysozyme
    Biophys. J., Vol. 92, No. 7. (1 April 2007), pp. L49-51.
    by Mehdi B Hamaneh, Matthias Buck
    posted to solvation implicit 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
    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 3 people skoddet apaydin jwm
  • Explicit and implicit water simulations of a &bgr;-hairpin peptide
    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
    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 3 people choonpeng RamuAnandakrishnan onufriev
  • Protein Folding in the Absence of the Solvent Ordering Contribution to the Hydrophobic Interaction
    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 solvent protein_design 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
    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.
    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 2 people apaydin cat_worth
  • De Novo Protein Design. I. In Search of Stability and Specificity
    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
    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
    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
    Nucl. Acids Res., Vol. 7, No. 2. (25 September 1979), pp. 517-528.
    by II Nikolskaya, NG Lopatina, NV Anikeicheva, SS Debov
    posted to methylation by msuarezdiez on 2008-06-06 10:29:09 as *
  • CpG Methylation Modifies the Genetic Stability of Cloned Repeat Sequences
    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
    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
    Genome Res., Vol. 16, No. 5. (1 May 2006), pp. 644-655.
    by Pooja Rawal, Veera B Kummarasetti, Jinoy Ravindran, 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.
    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
    Journal of Molecular Biology (September 1999), pp. 19-37.
    by ST Liang, M Bipatnath, YC Xu, SL 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.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by JD Sander, P Zaback, JK Joung, DF Voytas, D Dobbs
    posted to zinc_fingers by msuarezdiez on 2008-05-22 10:51:03 as ** along with 1 person austin
  • Function of the zinc finger in Escherichia coli Fpg protein
    J. Biol. Chem., Vol. 268, No. 35. (15 December 1993), pp. 26738-26744.
    by J Tchou, ML Michaels, JH Miller, AP Grollman
    posted to zinc_fingers_ecoli by msuarezdiez on 2008-05-19 15:43:35 as **
  • DksA affects ppGpp induction of RpoS at a translational level.
    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
    Nature Methods, Vol. 3, No. 8. (21 July 2006), pp. 623-628.
    by Alon Zaslaver, Anat Bren, Michal Ronen, 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
    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
    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 **
  • Toward rules relating zinc finger protein sequences and DNA binding site preferences.
    Proc Natl Acad Sci U S A, Vol. 89, No. 16. (15 August 1992), pp. 7345-7349.
    by JR Desjarlais, JM Berg
    posted to zinc_fingers by msuarezdiez on 2008-05-15 09:56:55 as ** along with 1 person aalibes
  • Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 6. (16 March 1999), pp. 2758-2763.
    by DJ Segal, B Dreier, RR Beerli, CF Barbas
    posted to zinc_fingers by msuarezdiez on 2008-05-15 09:53:08 as read
  • A synthetic oscillatory network of transcriptional regulators.
    Nature, Vol. 403, No. 6767. (20 January 2000), pp. 335-338.
    by MB Elowitz, S Leibler
    posted to no-tag by msuarezdiez on 2008-05-14 17:53:02 as read along with 11 people Borelli dagmar jjray austin tvdbulck rklancer dgront sharatjv mhucka margaritis Grobi
  • Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements.
    Nucleic Acids Res, Vol. 25, No. 6. (15 March 1997), pp. 1203-1210.
    by R Lutz, H Bujard
    posted to promoter_library by msuarezdiez on 2008-05-14 17:48:21 as * along with 1 person dbikard
  • De novo protein design using pairwise potentials and a genetic algorithm
    Protein Sci, Vol. 3, No. 4. (1 April 1994), pp. 567-574.
    by DT Jones
    posted to computational_protein_design bioinformatics by msuarezdiez on 2008-04-29 10:23:05 as **
  • The rational design of allosteric interactions in a monomeric protein and its applications to the construction of biosensors.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 94, No. 9. (29 April 1997), pp. 4366-4371.
    by JS Marvin, EE Corcoran, NA Hattangadi, JV Zhang, SA Gere, HW Hellinga
    posted to computational_protein_design biosensor by msuarezdiez on 2008-04-25 10:19:53 as **
  • Recent advances in the bioremediation of persistent organic pollutants via biomolecular engineering
    Enzyme and Microbial Technology, Vol. 37, No. 5. (3 October 2005), pp. 487-496.
    by Ee L Ang, Huimin Zhao, Jeffrey P Obbard
    posted to enzyme_design bioremediation by msuarezdiez on 2008-04-25 10:05:23 as **
  • Protein structure prediction by global optimization of a potential energy function
    Proceedings of the National Academy of Sciences, Vol. 96, No. 10. (11 May 1999), pp. 5482-5485.
    by Adam Liwo, Jooyoung Lee, Daniel R Ripoll, Jaroslaw Pillardy, Harold A Scheraga
    posted to computational_protein_design by msuarezdiez on 2008-04-24 17:38:09 as ***
  • Optimal Sequence Selection in Proteins of Known Structure by Simulated Evolution
    Proceedings of the National Academy of Sciences, Vol. 91, No. 13. (21 June 1994), pp. 5803-5807.
    by HW Hellinga, FM Richards
    posted to computational_protein_design by msuarezdiez on 2008-04-22 12:49:03 as read
  • Enhancing catalytic promiscuity for biocatalysis.
    Curr Opin Chem Biol, Vol. 9, No. 2. (April 2005), pp. 195-201.
    by RJ Kazlauskas
    posted to enzyme_design opinion by msuarezdiez on 2008-04-22 11:59:01 as ** along with 1 person robert
  • Automatic sequence design of MHC Class-I binding peptides impairing CD8+ T cell recognition
    J. Biol. Chem. (30 October 2002), M206853200.
    by Koji Ogata, Alfonso Jaramillo, William Cohen, Jean-Paul Briand, Francine Connan, Jeannine Choppin, Sylviane Muller, Shoshana J Wodak
    posted to computational_protein_design enzyme_design by msuarezdiez on 2008-04-22 11:51:18 as read
  • Engineered antibody Fc variants with enhanced effector function.
    Proc Natl Acad Sci U S A, Vol. 103, No. 11. (14 March 2006), pp. 4005-4010.
    by GA Lazar, W Dang, S Karki, O Vafa, JS Peng, L Hyun, C Chan, HS Chung, A Eivazi, SC Yoder, J Vielmetter, DF Carmichael, RJ Hayes, BI Dahiyat
    posted to computational_protein_design enzyme_design by msuarezdiez on 2008-04-22 11:44:41 as *** along with 1 person bilab
  • De Novo Computational Design of Retro-Aldol Enzymes
    Science, Vol. 319, No. 5868. (7 March 2008), pp. 1387-1391.
    by Lin Jiang, Eric A Althoff, Fernando R Clemente, 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 computational_protein_design enzyme_design by msuarezdiez on 2008-04-22 11:41:11 as ***** along with 12 people and 3 groups cambray joseph_x_zhou ucbcjbm barry aalibes jwm aprasad dgront zwang sobolevnrm davidlott scienbox McCammon structural_bioinformatics baker-group
  • Kemp elimination catalysts by computational enzyme design
    Nature (19 March 2008)
    by Daniela Röthlisberger, Olga Khersonsky, Andrew M Wollacott, Lin Jiang, Jason Dechancie, Jamie Betker, Jasmine L Gallaher, Eric A Althoff, Alexandre Zanghellini, Orly Dym, Shira Albeck, Kendall N Houk, Dan S Tawfik, David Baker
    posted to computational desig protein by msuarezdiez on 2008-04-22 11:27:04 as ***** along with 5 people and 1 group sobolevnrm austin neils cactus jwm baker-group
  • Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
    Genome Biology, Vol. 8 (21 February 2007), R22.
    by Carleton L Kingsford, Kunmi Ayanbule, Steven L Salzberg
    posted to transcriptional-terminators by msuarezdiez on 2008-04-04 16:15:22 as read along with 1 person treangen
  • Enzyme promiscuity: mechanism and applications
    Trends in Biotechnology, Vol. In Press, Corrected Proof
    by Karl Hult, Per Berglund
    posted to enzyme promiscuity by msuarezdiez on 2008-03-31 15:31:20 as ** along with 2 people Jporci tny
  • Directed evolution of a (beta alpha)8-barrel enzyme to catalyze related reactions in two different metabolic pathways.
    Proc Natl Acad Sci U S A, Vol. 97, No. 18. (29 August 2000), pp. 9925-9930.
    by C Jürgens, A Strom, D Wegener, S Hettwer, M Wilmanns, R Sterner
    posted to enzyme evolvability promiscuity by msuarezdiez on 2008-03-31 14:53:38 as **
  • Engineering a multipurpose catalyst.
    Nat Chem Biol, Vol. 2, No. 10. (October 2006), pp. 514-515.
    by RJ Kazlauskas
    posted to enzyme multipurpose promiscuity by msuarezdiez on 2008-03-31 14:11:18 as **
  • New formulae for folding catalysts make them multi-purpose enzymes
    Biotechnology and Bioengineering, Vol. 56, No. 6. (1997), pp. 645-649.
    by Mireille Moutiez, Régine Guthapfel, Paul Gueguen, Eric Quéméneur
    posted to ezyme promiscuity by msuarezdiez on 2008-03-31 14:05:48 as **
  • De novo design of catalytic proteins.
    Proc Natl Acad Sci U S A, Vol. 101, No. 32. (10 August 2004), pp. 11566-11570.
    by J Kaplan, WF DeGrado
    posted to design enzyme protein by msuarezdiez on 2008-03-31 13:45:51 as **** along with 1 person dgront
  • Creation of a Broad-Range and Highly Stereoselective D-Amino Acid Dehydrogenase for the One-Step Synthesis of D-Amino Acids
    J. Am. Chem. Soc., Vol. 128, No. 33. (23 August 2006), pp. 10923-10929.
    by K Vedha-Peters, M Gunawardana, JD Rozzell, SJ Novick
    posted to d-aminoacids enantiomers enzyme promiscuity by msuarezdiez on 2008-03-31 13:37:13 as **
  • Computational Protein Design: A Novel Path to Future Protein Drugs
    pp. 3973-3997.
    by M Rosenberg
    posted to computational desing protein by msuarezdiez on 2008-03-27 12:24:26 as **
  • Advances in computational protein design
    Current Opinion in Structural Biology, Vol. 14, No. 4. (August 2004), pp. 487-494.
    by Sheldon Park, Xi Yang, Jeffery G Saven
    posted to protein_design by msuarezdiez on 2008-03-27 12:23:05 as ** along with 1 person and 1 group allPowerde The_Festival_of_Doubt
  • Review: Protein Design--Where We Were, Where We Are, Where We're Going
    Journal of Structural Biology, Vol. 134, No. 2-3. (May 2001), pp. 269-281.
    by Navin Pokala, Tracy M Handel
    posted to computational design protein review by msuarezdiez on 2008-03-27 12:19:10 as ** along with 2 people joseph_x_zhou medic0747
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