Literature DB >> 20717908

An exciting but challenging road ahead for computational enzyme design.

David Baker1.   

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Year:  2010        PMID： 20717908      PMCID： PMC2998717          DOI： 10.1002/pro.481

Source DB:  PubMed          Journal:  Protein Sci        ISSN： 0961-8368            Impact factor:   6.725


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  14 in total

Review 1.  The depth of chemical time and the power of enzymes as catalysts.

Authors:  R Wolfenden; M J Snider
Journal:  Acc Chem Res       Date:  2001-12       Impact factor: 22.384

Review 2.  Critical analysis of antibody catalysis.

Authors:  D Hilvert
Journal:  Annu Rev Biochem       Date:  2000       Impact factor: 23.643

3.  Design of a novel globular protein fold with atomic-level accuracy.

Authors:  Brian Kuhlman; Gautam Dantas; Gregory C Ireton; Gabriele Varani; Barry L Stoddard; David Baker
Journal:  Science       Date:  2003-11-21       Impact factor: 47.728

Review 4.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

5.  Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.

Authors:  Justin B Siegel; Alexandre Zanghellini; Helena M Lovick; Gert Kiss; Abigail R Lambert; Jennifer L St Clair; Jasmine L Gallaher; Donald Hilvert; Michael H Gelb; Barry L Stoddard; Kendall N Houk; Forrest E Michael; David Baker
Journal:  Science       Date:  2010-07-16       Impact factor: 47.728

6.  Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field.

Authors:  Jianhan Chen; Wonpil Im; Charles L Brooks
Journal:  J Am Chem Soc       Date:  2006-03-22       Impact factor: 15.419

Review 7.  Advances in laboratory evolution of enzymes.

Authors:  Shimon Bershtein; Dan S Tawfik
Journal:  Curr Opin Chem Biol       Date:  2008-03-07       Impact factor: 8.822

8.  Kemp elimination catalysts by computational enzyme design.

Authors:  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
Journal:  Nature       Date:  2008-03-19       Impact factor: 49.962

9.  Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods.

Authors:  Vladimir Hnizdo; Jun Tan; Benjamin J Killian; Michael K Gilson
Journal:  J Comput Chem       Date:  2008-07-30       Impact factor: 3.376

10.  Analysis of the class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase at 0.99A resolution.

Authors:  Andreas Heine; John G Luz; Chi-Huey Wong; Ian A Wilson
Journal:  J Mol Biol       Date:  2004-10-29       Impact factor: 5.469
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  68 in total

1.  Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution.

Authors:  Olga Khersonsky; Daniela Röthlisberger; Andrew M Wollacott; Paul Murphy; Orly Dym; Shira Albeck; Gert Kiss; K N Houk; David Baker; Dan S Tawfik
Journal:  J Mol Biol       Date:  2011-01-28       Impact factor: 5.469

2.  Creating novel protein scripts beyond natural alphabets.

Authors:  Anil Kumar; Vibin Ramakrishnan
Journal:  Syst Synth Biol       Date:  2011-03-01

3.  Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59.

Authors:  Olga Khersonsky; Gert Kiss; Daniela Röthlisberger; Orly Dym; Shira Albeck; Kendall N Houk; David Baker; Dan S Tawfik
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-08       Impact factor: 11.205

4.  Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.

Authors:  Sagar D Khare; Yakov Kipnis; Per Greisen; Ryo Takeuchi; Yacov Ashani; Moshe Goldsmith; Yifan Song; Jasmine L Gallaher; Israel Silman; Haim Leader; Joel L Sussman; Barry L Stoddard; Dan S Tawfik; David Baker
Journal:  Nat Chem Biol       Date:  2012-02-05       Impact factor: 15.040

Review 5.  Optimizing non-natural protein function with directed evolution.

Authors:  Eric M Brustad; Frances H Arnold
Journal:  Curr Opin Chem Biol       Date:  2010-12-23       Impact factor: 8.822

6.  Elementary tetrahelical protein design for diverse oxidoreductase functions.

Authors:  Tammer A Farid; Goutham Kodali; Lee A Solomon; Bruce R Lichtenstein; Molly M Sheehan; Bryan A Fry; Chris Bialas; Nathan M Ennist; Jessica A Siedlecki; Zhenyu Zhao; Matthew A Stetz; Kathleen G Valentine; J L Ross Anderson; A Joshua Wand; Bohdana M Discher; Christopher C Moser; P Leslie Dutton
Journal:  Nat Chem Biol       Date:  2013-10-13       Impact factor: 15.040

Review 7.  Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution.

Authors:  Hans Renata; Z Jane Wang; Frances H Arnold
Journal:  Angew Chem Int Ed Engl       Date:  2015-02-03       Impact factor: 15.336

8.  Restricted sidechain plasticity in the structures of native proteins and complexes.

Authors:  Sarel J Fleishman; Sagar D Khare; Nobuyasu Koga; David Baker
Journal:  Protein Sci       Date:  2011-04       Impact factor: 6.725

9.  The use of ene adducts to study and engineer enoyl-thioester reductases.

Authors:  Raoul G Rosenthal; Bastian Vögeli; Nick Quade; Guido Capitani; Patrick Kiefer; Julia A Vorholt; Marc-Olivier Ebert; Tobias J Erb
Journal:  Nat Chem Biol       Date:  2015-04-13       Impact factor: 15.040

10.  Dissecting enzyme function with microfluidic-based deep mutational scanning.

Authors:  Philip A Romero; Tuan M Tran; Adam R Abate
Journal:  Proc Natl Acad Sci U S A       Date:  2015-05-26       Impact factor: 11.205
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