scholarly journals Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics

2018 ◽  
Vol 14 (12) ◽  
pp. e1006342 ◽  
Author(s):  
John M. Jumper ◽  
Nabil F. Faruk ◽  
Karl F. Freed ◽  
Tobin R. Sosnick
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Side Chain ◽  
Accurate Calculation ◽  
Chain Packing ◽  
Protein Molecular Dynamics ◽  
Side Chain Packing

scholarly journals Accurate calculation of the absolute free energy of binding for drug molecules

2016 ◽  
Vol 7 (1) ◽  
pp. 207-218 ◽  
Author(s):  
Matteo Aldeghi ◽  
Alexander Heifetz ◽  
Michael J. Bodkin ◽  
Stefan Knapp ◽  
Philip C. Biggin
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Free Energy Calculations ◽  
Accurate Calculation ◽  
Energy Calculations ◽  
Thermodynamic Cycles ◽  
Drug Molecules ◽  
The Absolute ◽  
Free Energy Of Binding

Free energy calculations based on molecular dynamics and thermodynamic cycles accurately reproduce experimental affinities of diverse bromodomain inhibitors.

Side Chain Packing of the N- and C-Terminal Helices Plays a Critical Role in the Kinetics of CytochromecFolding†

Biochemistry ◽  
1996 ◽  
Vol 35 (17) ◽  
pp. 5538-5549 ◽  
Author(s):  
Wilfredo Colón ◽  
Gülnur A. Elöve ◽  
L. Paul Wakem ◽  
Fred Sherman ◽  
Heinrich Roder
Keyword(s):  
Critical Role ◽  
Side Chain ◽  
Chain Packing ◽  
Kinetics Of ◽  
Side Chain Packing

scholarly journals Side-chain Packing Using SE(3)-Transformer

2021 ◽  
Author(s):  
Akhil Jindal ◽  
Sergei Kotelnikov ◽  
Dzmitry Padhorny ◽  
Dima Kozakov ◽  
Yimin Zhu ◽  
...  
Keyword(s):  
Side Chain ◽  
Chain Packing ◽  
Side Chain Packing

scholarly journals OPUS-DOSP: A Distance- and Orientation-Dependent All-Atom Potential Derived from Side-Chain Packing

2017 ◽  
Vol 429 (20) ◽  
pp. 3113-3120 ◽  
Author(s):  
Gang Xu ◽  
Tianqi Ma ◽  
Tianwu Zang ◽  
Weitao Sun ◽  
Qinghua Wang ◽  
...  
Keyword(s):  
Side Chain ◽  
Chain Packing ◽  
Atom Potential ◽  
Side Chain Packing
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