EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization

2007 ◽  
Vol 67 (4) ◽  
pp. 1010-1025 ◽  
Author(s):  
Aurélien Grosdidier ◽  
Vincent Zoete ◽  
Olivier Michielin
Keyword(s):  
Small Molecules ◽  
Active Sites ◽  
Evolutionary Optimization ◽  
Protein Active Sites

scholarly journals The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?

2020 ◽  
Author(s):  
Richard T Bradshaw ◽  
Jacek Dziedzic ◽  
Chris-Kriton Skylaris ◽  
Jonathan W. Essex
Keyword(s):  
Electric Fields ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Force Fields ◽  
Prolyl Isomerase ◽  
Peptidyl Prolyl Isomerase ◽  
Polarizable Force Field ◽  
Polarizable Force Fields ◽  
Protein Active Sites ◽  
Dynamics Simulations

<div><div><div><p>Preorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric fields present inside the active site of the peptidyl-prolyl isomerase cyclophilin A. We compare the molecular mechanical electric fields to those calculated with a fully first principles quantum mechanical (QM) representation of the protein, solvent, and ions, and find that AMOEBA consistently shows far greater correlation with the QM electric fields than either of the additive force fields tested. Catalytically-relevant fields calculated with AMOEBA were typically smaller than those observed with additive potentials, but were generally consistent with an electrostatically-driven mechanism for catalysis. Our results highlight the accuracy and the potential advantages of using polarizable force fields in systems where accurate electrostatics may be crucial for providing mechanistic insights.</p></div></div></div>

Vicinity analysis: a methodology for the identification of similar protein active sites

2008 ◽  
Vol 15 (5) ◽  
pp. 489-498 ◽  
Author(s):  
A. McGready ◽  
A. Stevens ◽  
M. Lipkin ◽  
B. D. Hudson ◽  
D. C. Whitley ◽  
...  
Keyword(s):  
Active Sites ◽  
Similar Protein ◽  
Protein Active Sites

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

2008 ◽  
Vol 17 (2) ◽  
pp. 333-341 ◽  
Author(s):  
Wenxu Tong ◽  
Ronald J. Williams ◽  
Ying Wei ◽  
Leonel F. Murga ◽  
Jaeju Ko ◽  
...  
Keyword(s):  
Support Vector Machines ◽  
Active Sites ◽  
Support Vector ◽  
Protein Active Sites ◽  
Vector Machines

scholarly journals The Solution Structure of [Cu(aq)]2+and Its Implications for Rack-Induced Bonding in Blue Copper Protein Active Sites

2007 ◽  
Vol 46 (18) ◽  
pp. 7684-7684 ◽  
Author(s):  
Patrick Frank ◽  
Maurizio Benfatto ◽  
Robert K. Szilagyi ◽  
Paola D'Angelo ◽  
Stefano Della Longa ◽  
...  
Keyword(s):  
Active Sites ◽  
Solution Structure ◽  
Blue Copper Protein ◽  
Blue Copper ◽  
Copper Protein ◽  
Protein Active Sites

Understanding the oxidation chemistry of copper protein active sites: Copper complexes that activate dioxygen or stablize phenoxyl radicals

1997 ◽  
Vol 67 (1-4) ◽  
pp. 38
Author(s):  
Jason A. Halfen ◽  
Samiran Mahapatra ◽  
Lisa Berreau ◽  
Brian A. Jazdzwski ◽  
Victor G. Young ◽  
...  
Keyword(s):  
Active Sites ◽  
Copper Complexes ◽  
Phenoxyl Radicals ◽  
Copper Protein ◽  
Protein Active Sites ◽  
Oxidation Chemistry

The Solution Structure of [Cu(aq)]2+and Its Implications for Rack-Induced Bonding in Blue Copper Protein Active Sites

2005 ◽  
Vol 44 (6) ◽  
pp. 1922-1933 ◽  
Author(s):  
Patrick Frank ◽  
Maurizio Benfatto ◽  
Robert K. Szilagyi ◽  
Paola D'Angelo ◽  
Stefano Della Longa ◽  
...  
Keyword(s):  
Active Sites ◽  
Solution Structure ◽  
Blue Copper Protein ◽  
Blue Copper ◽  
Copper Protein ◽  
Protein Active Sites
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