SurfPB: A GPU-Accelerated Electrostatic Calculation and Visualization Tool for Biomolecules
In this work, we present SurfPB as a useful tool for the study of biomolecules. It can do many typical calculations, including the molecular surface, electrostatic potential, solvation free energy, entropy, and binding free energy. Among all of the calculations, the entropy calculation is the most t...
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| Veröffentlicht in: | Journal of chemical information and modeling 2023-08, Vol.63 (15), p.4490-4496 |
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| container_title | Journal of chemical information and modeling |
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| creator | Liao, Jun Shu, Zirui Gao, Junyong Wu, Mincong Chen, Changjun |
| description | In this work, we present SurfPB as a useful tool for the study of biomolecules. It can do many typical calculations, including the molecular surface, electrostatic potential, solvation free energy, entropy, and binding free energy. Among all of the calculations, the entropy calculation is the most time-consuming one. In SurfPB, the calculation can be performed in a vacuum or implicit solvent and accelerated on GPU. The Poisson–Boltzmann equation solver is accelerated on GPU as well. Moreover, we developed a graphical user interface for SurfPB. It allows users to input the parameters and complete the whole calculation in a visual way. The calculated electrostatic potentials are shown on the molecular surface in a three-dimensional scene. |
| doi_str_mv | 10.1021/acs.jcim.3c00745 |
| format | Article |
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The calculated electrostatic potentials are shown on the molecular surface in a three-dimensional scene.</description><subject>Biomolecules</subject><subject>Boltzmann transport equation</subject><subject>Entropy</subject><subject>Free energy</subject><subject>Graphical user interface</subject><subject>Mathematical analysis</subject><subject>Solvation</subject><issn>1549-9596</issn><issn>1549-960X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><recordid>eNp1kMFLwzAUh4Mobk7vnqTgxYOdL2nTLt62MacwcOAmgoeSpil0pM1MmoP-9WZ28yB4yuPx_V7e-xC6xDDEQPAdF3a4EVU9jARAGtMj1Mc0ZiFL4O34UFOW9NCZtRuAKGIJOUW9KKUAFFgfvb84Uy4n98E4mC_X4VgIqaThrSyCmZKiNdq2vK1EMOVKOOVL3QS8KYLXyjquqq-us9JaBaU2waTStfZBp6Q9RyclV1Ze7N8BWj_MVtPHcPE8f5qOFyGPkrgNMeeikDkRkBSYJBwngpQRgIxSKXDK8ljklI4wYxTHAhMMBSfE9wqcJrJk0QDddHO3Rn84adusrqy_Q_FGamczMqKQEmAYe_T6D7rRzjR-u46iXsyOgo4S_nxrZJltTVVz85lhyHbiMy8-24nP9uJ95Go_2OW1LH4DB9MeuO2An-jh03_nfQPXHo4z</recordid><startdate>20230814</startdate><enddate>20230814</enddate><creator>Liao, Jun</creator><creator>Shu, Zirui</creator><creator>Gao, Junyong</creator><creator>Wu, Mincong</creator><creator>Chen, Changjun</creator><general>American Chemical Society</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SC</scope><scope>7SR</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>JQ2</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-6188-5223</orcidid></search><sort><creationdate>20230814</creationdate><title>SurfPB: A GPU-Accelerated Electrostatic Calculation and Visualization Tool for Biomolecules</title><author>Liao, Jun ; Shu, Zirui ; Gao, Junyong ; Wu, Mincong ; Chen, Changjun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a364t-1aacdeb2c06d126a16c2f300e37ec179b4cb558199514c1210da22cb5d176ef93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Biomolecules</topic><topic>Boltzmann transport equation</topic><topic>Entropy</topic><topic>Free energy</topic><topic>Graphical user interface</topic><topic>Mathematical analysis</topic><topic>Solvation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Liao, Jun</creatorcontrib><creatorcontrib>Shu, Zirui</creatorcontrib><creatorcontrib>Gao, Junyong</creatorcontrib><creatorcontrib>Wu, Mincong</creatorcontrib><creatorcontrib>Chen, Changjun</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Computer and Information Systems Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of chemical information and modeling</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Liao, Jun</au><au>Shu, Zirui</au><au>Gao, Junyong</au><au>Wu, Mincong</au><au>Chen, Changjun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>SurfPB: A GPU-Accelerated Electrostatic Calculation and Visualization Tool for Biomolecules</atitle><jtitle>Journal of chemical information and modeling</jtitle><addtitle>J. Chem. Inf. Model</addtitle><date>2023-08-14</date><risdate>2023</risdate><volume>63</volume><issue>15</issue><spage>4490</spage><epage>4496</epage><pages>4490-4496</pages><issn>1549-9596</issn><eissn>1549-960X</eissn><abstract>In this work, we present SurfPB as a useful tool for the study of biomolecules. It can do many typical calculations, including the molecular surface, electrostatic potential, solvation free energy, entropy, and binding free energy. Among all of the calculations, the entropy calculation is the most time-consuming one. In SurfPB, the calculation can be performed in a vacuum or implicit solvent and accelerated on GPU. The Poisson–Boltzmann equation solver is accelerated on GPU as well. Moreover, we developed a graphical user interface for SurfPB. It allows users to input the parameters and complete the whole calculation in a visual way. 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| language | eng |
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| source | ACS Publications |
| subjects | Biomolecules Boltzmann transport equation Entropy Free energy Graphical user interface Mathematical analysis Solvation |
| title | SurfPB: A GPU-Accelerated Electrostatic Calculation and Visualization Tool for Biomolecules |
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