Protein molecular dynamics with the generalized born/ACE solvent model

Nicolas Calimet; Michael Schaefer; Thomas Simonson

doi:10.1002/prot.1134

Protein molecular dynamics with the generalized born/ACE solvent model

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.1134 ◽

2001 ◽

Vol 45 (2) ◽

pp. 144-158 ◽

Cited By ~ 78

Author(s):

Nicolas Calimet ◽

Michael Schaefer ◽

Thomas Simonson

Keyword(s):

Molecular Dynamics ◽

Generalized Born ◽

Solvent Model ◽

Protein Molecular Dynamics

Get full-text (via PubEx)

Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized born implicit-solvent model

Journal of Computational Chemistry ◽

10.1002/jcc.21813 ◽

2011 ◽

Vol 32 (11) ◽

pp. 2348-2358 ◽

Cited By ~ 15

Author(s):

Yuhang Wang ◽

Jason A. Wallace ◽

Peter H. Koenig ◽

Jana K. Shen

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Nonionic Surfactant ◽

Implicit Solvent ◽

Generalized Born ◽

Surfactant Micelles ◽

Implicit Solvent Model ◽

Solvent Model ◽

Dynamics Simulations

Get full-text (via PubEx)

Distinguish protein decoys by Using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.10470 ◽

2004 ◽

Vol 55 (3) ◽

pp. 620-634 ◽

Cited By ~ 217

Author(s):

Mathew C. Lee ◽

Yong Duan

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Scoring Function ◽

Generalized Born ◽

Amber Force Field ◽

Solvent Model ◽

Dynamics Simulations

Get full-text (via PubEx)

Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units

Journal of Computational Chemistry ◽

10.1002/jcc.26133 ◽

2019 ◽

Vol 41 (8) ◽

pp. 830-838 ◽

Cited By ~ 1

Author(s):

Xiping Gong ◽

Mara Chiricotto ◽

Xiaorong Liu ◽

Erik Nordquist ◽

Michael Feig ◽

...

Keyword(s):

Graphics Processing Units ◽

Accessible Surface Area ◽

Solvent Accessible Surface Area ◽

Molecular Volume ◽

Implicit Solvent ◽

Generalized Born ◽

Solvent Model ◽

Accessible Surface ◽

Graphics Processing ◽

Solvent Accessible Surface

Get full-text (via PubEx)

Molecular Dynamics Calculation of Interaction Forces between Colloids in Aqueous Electrolyte Solutions Using an Implicit Solvent Model

KAGAKU KOGAKU RONBUNSHU ◽

10.1252/kakoronbunshu.31.295 ◽

2005 ◽

Vol 31 (5) ◽

pp. 295-300 ◽

Cited By ~ 1

Author(s):

Shintaro Morisada ◽

Kenji Muranishi ◽

Hiroyuki Shinto ◽

Ko Higashitani

Keyword(s):

Molecular Dynamics ◽

Aqueous Electrolyte ◽

Electrolyte Solutions ◽

Implicit Solvent ◽

Interaction Forces ◽

Implicit Solvent Model ◽

Aqueous Electrolyte Solutions ◽

Solvent Model ◽

Dynamics Calculation

Get full-text (via PubEx)

Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model

Journal of the American Chemical Society ◽

10.1021/ja9939385 ◽

2000 ◽

Vol 122 (11) ◽

pp. 2489-2498 ◽

Cited By ~ 291

Author(s):

Vickie Tsui ◽

David A. Case

Keyword(s):

Molecular Dynamics ◽

Nucleic Acids ◽

Molecular Dynamics Simulations ◽

Solvation Model ◽

Generalized Born ◽

Dynamics Simulations

Get full-text (via PubEx)

Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model

Journal of Computational Chemistry ◽

10.1002/(sici)1096-987x(19990715)20:9<956::aid-jcc7>3.0.co;2-r ◽

1999 ◽

Vol 20 (9) ◽

pp. 956-970 ◽

Cited By ~ 4

Author(s):

Michael J. Potter ◽

Paul D. Kirchhoff ◽

Heather A. Carlson ◽

J. Andrew McCammon

Keyword(s):

Molecular Dynamics ◽

Continuum Solvent Model ◽

Solvent Model

Get full-text (via PubEx)

Cyclic trimer of human cystatin C, an amyloidogenic protein - molecular dynamics and experimental studies

Journal of Applied Physics ◽

10.1063/1.5023807 ◽

2018 ◽

Vol 123 (17) ◽

pp. 174701 ◽

Cited By ~ 2

Author(s):

Magdalena Chrabąszczewska ◽

Martyna Maszota-Zieleniak ◽

Zuzanna Pietralik ◽

Michał Taube ◽

Sylwia Rodziewicz-Motowidło ◽

...

Keyword(s):

Molecular Dynamics ◽

Cystatin C ◽

Experimental Studies ◽

Cyclic Trimer ◽

Human Cystatin C ◽

Amyloidogenic Protein ◽

Protein Molecular Dynamics ◽

Human Cystatin

Get full-text (via PubEx)

Detecting Native Protein Folds among Large Decoy Sets with the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model

Computational Methods for Protein Folding - Advances in Chemical Physics ◽

10.1002/0471224421.ch8 ◽

2002 ◽

pp. 459-486 ◽

Cited By ~ 1

Author(s):

Anders Wallqvist ◽

Emilio Gallicchio ◽

Anthony K. Felts ◽

Ronald M. Levy

Keyword(s):

Native Protein ◽

Generalized Born ◽

Protein Folds ◽

Solvent Model ◽

Atom Potential

Get full-text (via PubEx)

Fold Recognition using the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model

Lecture Notes in Computational Science and Engineering - Computational Methods for Macromolecules: Challenges and Applications ◽

10.1007/978-3-642-56080-4_18 ◽

2002 ◽

pp. 445-476

Author(s):

Anthony K. Felts ◽

Anders Wallqvist ◽

Emilio Gallicchio ◽

Donna Bassolino ◽

Stanley R. Krystek ◽

...

Keyword(s):

Fold Recognition ◽

Generalized Born ◽

Solvent Model ◽

Atom Potential

Get full-text (via PubEx)

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

PLoS Computational Biology ◽

10.1371/journal.pcbi.1006342 ◽

2018 ◽

Vol 14 (12) ◽

pp. e1006342 ◽

Cited By ~ 3

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

Get full-text (via PubEx)