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Items: 1 to 20 of 123

1.

TransCent: computational enzyme design by transferring active sites and considering constraints relevant for catalysis.

Fischer A, Enkler N, Neudert G, Bocola M, Sterner R, Merkl R.

BMC Bioinformatics. 2009 Feb 10;10:54. doi: 10.1186/1471-2105-10-54.

2.

A novel method for enzyme design.

Zhu X, Lai L.

J Comput Chem. 2009 Jan 30;30(2):256-67. doi: 10.1002/jcc.21050.

PMID:
18615422
3.

Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies.

Nagao C, Nagano N, Mizuguchi K.

Proteins. 2010 Aug 1;78(10):2369-84. doi: 10.1002/prot.22750.

PMID:
20544971
4.

Analysis of catalytic residues in enzyme active sites.

Bartlett GJ, Porter CT, Borkakoti N, Thornton JM.

J Mol Biol. 2002 Nov 15;324(1):105-21.

PMID:
12421562
5.

An improved prediction of catalytic residues in enzyme structures.

Tang YR, Sheng ZY, Chen YZ, Zhang Z.

Protein Eng Des Sel. 2008 May;21(5):295-302. doi: 10.1093/protein/gzn003.

6.

Automated scaffold selection for enzyme design.

Malisi C, Kohlbacher O, Höcker B.

Proteins. 2009 Oct;77(1):74-83. doi: 10.1002/prot.22418.

PMID:
19408301
7.

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.

Najmanovich R, Kurbatova N, Thornton J.

Bioinformatics. 2008 Aug 15;24(16):i105-11. doi: 10.1093/bioinformatics/btn263.

8.

Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures.

Gong S, Blundell TL.

PLoS Comput Biol. 2008 Oct 3;4(10):e1000179. doi: 10.1371/journal.pcbi.1000179.

9.

Systematic optimization model and algorithm for binding sequence selection in computational enzyme design.

Huang X, Han K, Zhu Y.

Protein Sci. 2013 Jul;22(7):929-41. doi: 10.1002/pro.2275.

10.

New algorithms and an in silico benchmark for computational enzyme design.

Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Röthlisberger D, Baker D.

Protein Sci. 2006 Dec;15(12):2785-94.

12.

Structure/function analysis of a dUTPase: catalytic mechanism of a potential chemotherapeutic target.

Harris JM, McIntosh EM, Muscat GE.

J Mol Biol. 1999 Apr 30;288(2):275-87.

PMID:
10329142
14.
15.

Computational design of a biologically active enzyme.

Dwyer MA, Looger LL, Hellinga HW.

Science. 2004 Jun 25;304(5679):1967-71. Retraction in: Dwyer MA, Looger LL, Hellinga HW. Science. 2008 Feb 1;319(5863):569.

16.

Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures.

Strömbergsson H, Kryshtafovych A, Prusis P, Fidelis K, Wikberg JE, Komorowski J, Hvidsten TR.

Proteins. 2006 Nov 15;65(3):568-79.

PMID:
16948162
17.

Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.

Roovers M, Oudjama Y, Kaminska KH, Purta E, Caillet J, Droogmans L, Bujnicki JM.

Proteins. 2008 Jun;71(4):2076-85. doi: 10.1002/prot.21918.

PMID:
18186482
18.

Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines.

Tong W, Williams RJ, Wei Y, Murga LF, Ko J, Ondrechen MJ.

Protein Sci. 2008 Feb;17(2):333-41.

19.
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