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@article{Miller2012, | ||
abstract = {MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo (MC) simulations. Several implicit solvation models are available with MMPBSA.py, including the Poisson-Boltzmann Model, the Generalized Born Model, and the Reference Interaction Site Model. Vibrational frequencies may be calculated using normal mode or quasi-harmonic analysis to approximate the solute entropy. Specific interactions can also be dissected using free energy decomposition or alanine scanning. A parallel implementation significantly speeds up the calculation by dividing frames evenly across available processors. MMPBSA.py is an efficient, user-friendly program with the flexibility to accommodate the needs of users performing end-state free energy calculations. The source code can be downloaded at http://ambermd.org/ with AmberTools, released under the GNU General Public License.}, | ||
author = {Miller, Bill R 3rd and McGee, T Dwight Jr and Swails, Jason M and Homeyer, Nadine and Gohlke, Holger and Roitberg, Adrian E}, | ||
doi = {10.1021/ct300418h}, | ||
issn = {1549-9618 (Print)}, | ||
journal = {Journal of chemical theory and computation}, | ||
language = {eng}, | ||
month = {sep}, | ||
number = {9}, | ||
pages = {3314--3321}, | ||
pmid = {26605738}, | ||
title = {{MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.}}, | ||
volume = {8}, | ||
year = {2012} | ||
} |
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TY - JOUR | ||
T1 - MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. | ||
A1 - Miller, Bill R 3rd | ||
A1 - McGee, T Dwight Jr | ||
A1 - Swails, Jason M | ||
A1 - Homeyer, Nadine | ||
A1 - Gohlke, Holger | ||
A1 - Roitberg, Adrian E | ||
Y1 - 2012/09// | ||
JF - Journal of chemical theory and computation | ||
VL - 8 | ||
LA - eng | ||
IS - 9 | ||
SP - 3314 | ||
EP - 3321 | ||
DO - 10.1021/ct300418h | ||
N2 - MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo (MC) simulations. Several implicit solvation models are available with MMPBSA.py, including the Poisson-Boltzmann Model, the Generalized Born Model, and the Reference Interaction Site Model. Vibrational frequencies may be calculated using normal mode or quasi-harmonic analysis to approximate the solute entropy. Specific interactions can also be dissected using free energy decomposition or alanine scanning. A parallel implementation significantly speeds up the calculation by dividing frames evenly across available processors. MMPBSA.py is an efficient, user-friendly program with the flexibility to accommodate the needs of users performing end-state free energy calculations. The source code can be downloaded at http://ambermd.org/ with AmberTools, released under the GNU General Public License. | ||
ER - |
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<?xml version="1.0" encoding="UTF-8"?><xml><records><record><database name="MMPBSA_py_citation.enl" path="MMPBSA_py_citation.enl">MMPBSA_py_citation.enl</database><ref-type name="Journal Article">0</ref-type><contributors><authors><author>Miller, Bill R 3rd</author><author>McGee, T Dwight Jr</author><author>Swails, Jason M</author><author>Homeyer, Nadine</author><author>Gohlke, Holger</author><author>Roitberg, Adrian E</author></authors></contributors><titles><title>MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.</title><secondary-title>Journal of chemical theory and computation</secondary-title></titles><periodical><full-title>Journal of chemical theory and computation</full-title></periodical><pages>3314-3321</pages><volume>8</volume><issue>9</issue><keywords/><dates><year>2012</year></dates><accession-num>26605738</accession-num><electronic-resource-num>10.1021/ct300418h</electronic-resource-num><language>eng</language><urls/><abstract>MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo (MC) simulations. Several implicit solvation models are available with MMPBSA.py, including the Poisson-Boltzmann Model, the Generalized Born Model, and the Reference Interaction Site Model. Vibrational frequencies may be calculated using normal mode or quasi-harmonic analysis to approximate the solute entropy. Specific interactions can also be dissected using free energy decomposition or alanine scanning. A parallel implementation significantly speeds up the calculation by dividing frames evenly across available processors. MMPBSA.py is an efficient, user-friendly program with the flexibility to accommodate the needs of users performing end-state free energy calculations. The source code can be downloaded at http://ambermd.org/ with AmberTools, released under the GNU General Public License.</abstract></record></records></xml> |
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