Search details
1.
EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions.
Nat Methods
; 20(10): 1516-1522, 2023 Oct.
Article
in English
| MEDLINE | ID: mdl-37735566
2.
Enzyme function and evolution through the lens of bioinformatics.
Biochem J
; 480(22): 1845-1863, 2023 11 29.
Article
in English
| MEDLINE | ID: mdl-37991346
3.
GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs.
Nucleic Acids Res
; 50(W1): W392-W397, 2022 07 05.
Article
in English
| MEDLINE | ID: mdl-35524575
4.
A global analysis of function and conservation of catalytic residues in enzymes.
J Biol Chem
; 295(2): 314-324, 2020 01 10.
Article
in English
| MEDLINE | ID: mdl-31796628
5.
GRaSP: a graph-based residue neighborhood strategy to predict binding sites.
Bioinformatics
; 36(Suppl_2): i726-i734, 2020 12 30.
Article
in English
| MEDLINE | ID: mdl-33381849
6.
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.
Nucleic Acids Res
; 46(D1): D618-D623, 2018 01 04.
Article
in English
| MEDLINE | ID: mdl-29106569
7.
Transform-MinER: transforming molecules in enzyme reactions.
Bioinformatics
; 34(20): 3597-3599, 2018 10 15.
Article
in English
| MEDLINE | ID: mdl-29762650
8.
cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.
Nucleic Acids Res
; 45(20): 11559-11569, 2017 Nov 16.
Article
in English
| MEDLINE | ID: mdl-29036576
9.
Unique Triphenylphosphonium Derivatives for Enhanced Mitochondrial Uptake and Photodynamic Therapy.
Bioconjug Chem
; 28(2): 590-599, 2017 02 15.
Article
in English
| MEDLINE | ID: mdl-28049291
10.
Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD).
J Phys Chem A
; 120(27): 5300-6, 2016 Jul 14.
Article
in English
| MEDLINE | ID: mdl-27128525
11.
New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models.
Arch Biochem Biophys
; 582: 107-15, 2015 Sep 15.
Article
in English
| MEDLINE | ID: mdl-25772386
12.
Synthesis and Hydrolytic Studies on the Air-Stable [(4-CN-PhO)(E)P(µ-N(t)Bu)]2 (E = O, S, and Se) Cyclodiphosphazanes.
Inorg Chem
; 54(13): 6423-32, 2015 Jul 06.
Article
in English
| MEDLINE | ID: mdl-26068578
13.
Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli.
Acta Crystallogr D Biol Crystallogr
; 70(Pt 5): 1297-310, 2014 May.
Article
in English
| MEDLINE | ID: mdl-24816099
14.
Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes.
J Comput Chem
; 34(24): 2079-90, 2013 Sep 15.
Article
in English
| MEDLINE | ID: mdl-23798313
15.
The catalytic mechanism of protein phosphatase 5 established by DFT calculations.
Chemistry
; 19(42): 14081-9, 2013 Oct 11.
Article
in English
| MEDLINE | ID: mdl-24014428
16.
The 3D Modules of Enzyme Catalysis: Deconstructing Active Sites into Distinct Functional Entities.
J Mol Biol
; 435(20): 168254, 2023 Oct 15.
Article
in English
| MEDLINE | ID: mdl-37652131
17.
The catalytic mechanism of HIV-1 integrase for DNA 3'-end processing established by QM/MM calculations.
J Am Chem Soc
; 134(32): 13436-47, 2012 Aug 15.
Article
in English
| MEDLINE | ID: mdl-22793648
18.
Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues.
J Mol Biol
; 434(7): 167517, 2022 04 15.
Article
in English
| MEDLINE | ID: mdl-35240125
19.
Using mechanism similarity to understand enzyme evolution.
Biophys Rev
; 14(6): 1273-1280, 2022 Dec.
Article
in English
| MEDLINE | ID: mdl-36659981
20.
The Enzyme Portal: an integrative tool for enzyme information and analysis.
FEBS J
; 289(19): 5875-5890, 2022 10.
Article
in English
| MEDLINE | ID: mdl-34437766