Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs

He Huang; Carlos Simmerling

doi:10.1021/acs.jctc.8b00413

Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.8b00413 ◽

2018 ◽

Vol 14 (11) ◽

pp. 5797-5814 ◽

Cited By ~ 5

Author(s):

He Huang ◽

Carlos Simmerling

Keyword(s):

Surface Area ◽

Accessible Surface Area ◽

Solvent Accessible Surface Area ◽

Implicit Solvent ◽

Accessible Surface ◽

Solvent Accessible Surface

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GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations

Journal of Chemical Theory and Computation ◽

10.1021/ct3003089 ◽

2012 ◽

Vol 8 (7) ◽

pp. 2521-2530 ◽

Cited By ~ 33

Author(s):

David E. Tanner ◽

James C. Phillips ◽

Klaus Schulten

Keyword(s):

Surface Area ◽

Accessible Surface Area ◽

Solvent Accessible Surface Area ◽

Implicit Solvent ◽

Generalized Born ◽

Accessible Surface ◽

Solvent Accessible Surface

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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

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Dependence of GC-RRTs on the solvent-accessible surface area of dioxins and related compounds

Chemosphere ◽

10.1016/s0045-6535(00)00510-5 ◽

2001 ◽

Vol 44 (6) ◽

pp. 1307-1314

Author(s):

Masakazu Makino

Keyword(s):

Surface Area ◽

Accessible Surface Area ◽

Solvent Accessible Surface Area ◽

Accessible Surface ◽

Solvent Accessible Surface ◽

Related Compounds

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Molecular Modeling of Surfactant Micellization Using Solvent-Accessible Surface Area

Langmuir ◽

10.1021/acs.langmuir.8b03440 ◽

2019 ◽

Vol 35 (6) ◽

pp. 2443-2450 ◽

Cited By ~ 7

Author(s):

Hsieh Chen ◽

Athanassios Z. Panagiotopoulos

Keyword(s):

Molecular Modeling ◽

Surface Area ◽

Accessible Surface Area ◽

Solvent Accessible Surface Area ◽

Accessible Surface ◽

Solvent Accessible Surface

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CUSA and CUDE: GPU-Accelerated Methods for Estimating Solvent Accessible Surface Area and Desolvation

Journal of Computational Biology ◽

10.1089/cmb.2008.0157 ◽

2009 ◽

Vol 16 (4) ◽

pp. 523-537 ◽

Cited By ~ 22

Author(s):

David Dynerman ◽

Erick Butzlaff ◽

Julie C. Mitchell

Keyword(s):

Surface Area ◽

Accessible Surface Area ◽

Solvent Accessible Surface Area ◽

Accelerated Methods ◽

Accessible Surface ◽

Solvent Accessible Surface

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Solvent accessible surface area approximations for rapid and accurate protein structure prediction

Journal of Molecular Modeling ◽

10.1007/s00894-009-0454-9 ◽

2009 ◽

Vol 15 (9) ◽

pp. 1093-1108 ◽

Cited By ~ 90

Author(s):

Elizabeth Durham ◽

Brent Dorr ◽

Nils Woetzel ◽

René Staritzbichler ◽

Jens Meiler

Keyword(s):

Protein Structure ◽

Surface Area ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Accessible Surface Area ◽

Solvent Accessible Surface Area ◽

Accessible Surface ◽

Solvent Accessible Surface

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Solvent Accessible Surface Area of Amino Acid Residues in Globular Proteins: Correlation of Apparent Transfer Free Energies with Experimental Hydrophobicity Scales

Biomacromolecules ◽

10.1021/bm8015169 ◽

2009 ◽

Vol 10 (5) ◽

pp. 1224-1237 ◽

Cited By ~ 16

Author(s):

Alexey K. Shaytan ◽

Konstantin V. Shaitan ◽

Alexei R. Khokhlov

Keyword(s):

Amino Acid ◽

Surface Area ◽

Accessible Surface Area ◽

Globular Proteins ◽

Solvent Accessible Surface Area ◽

Amino Acid Residues ◽

Free Energies ◽

Accessible Surface ◽

Solvent Accessible Surface

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Parallel computation of solvent accessible surface area of protein molecules

[1993] Proceedings Seventh International Parallel Processing Symposium ◽

10.1109/ipps.1993.262798 ◽

2002 ◽

Cited By ~ 4

Author(s):

E. Suh ◽

B.K. Lee ◽

R. Martino ◽

B. Narahari ◽

A. Choudhary

Keyword(s):

Parallel Computation ◽

Surface Area ◽

Accessible Surface Area ◽

Solvent Accessible Surface Area ◽

Protein Molecules ◽

Accessible Surface ◽

Solvent Accessible Surface

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Efficient algorithms for protein solvent accessible surface area

Proceedings Fourth International Conference/Exhibition on High Performance Computing in the Asia-Pacific Region ◽

10.1109/hpc.2000.843502 ◽

2000 ◽

Cited By ~ 1

Author(s):

N. Futamura ◽

S. Aluru ◽

D. Ranjan ◽

K. Mehrotra

Keyword(s):

Surface Area ◽

Accessible Surface Area ◽

Efficient Algorithms ◽

Solvent Accessible Surface Area ◽

Accessible Surface ◽

Solvent Accessible Surface

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Solvent accessible surface area and excluded volume in proteins

Journal of Molecular Biology ◽

10.1016/0022-2836(84)90231-6 ◽

1984 ◽

Vol 178 (1) ◽

pp. 63-89 ◽

Cited By ~ 419

Author(s):

Timothy J. Richmond

Keyword(s):

Surface Area ◽

Accessible Surface Area ◽

Solvent Accessible Surface Area ◽

Excluded Volume ◽

Accessible Surface ◽

Solvent Accessible Surface

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