FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4322718786> ?p ?o ?g. }

• W4322718786 endingPage "1549" @default.
• W4322718786 startingPage "1536" @default.
• W4322718786 abstract "Abstract Integral equation theory (IET) provides an effective solvation model for chemical and biological systems that balances computational efficiency and accuracy. We present a new software package, the expanded package for IET‐based solvation (EPISOL), that performs 3D‐reference interaction site model (3D‐RISM) calculations to obtain the solvation structure and free energies of solute molecules in different solvents. In EPISOL, we have implemented 22 different closures, multiple free energy functionals, and new variations of 3D‐RISM theory, including the recent hydrophobicity‐induced density inhomogeneity (HI) theory for hydrophobic solutes and ion‐dipole correction (IDC) theory for negatively charged solutes. To speed up the convergence and enhance the stability of the self‐consistent iterations, we have introduced several numerical schemes in EPISOL, including a newly developed dynamic mixing approach. We show that these schemes have significantly reduced the failure rate of 3D‐RISM calculations compared to AMBER‐RISM software. EPISOL consists of both a user‐friendly graphic interface and a kernel library that allows users to call its routines and adapt them to other programs. EPISOL is compatible with the force‐field and coordinate files from both AMBER and GROMACS simulation packages. Moreover, EPISOL is equipped with an internal memory control to efficiently manage the use of physical memory, making it suitable for performing calculations on large biomolecules. We demonstrate that EPISOL can efficiently and accurately calculate solvation density distributions around various solute molecules (including a protein chaperone consisting of 120,715 atoms) and obtain solvent free energy for a wide range of organic compounds. We expect that EPISOL can be widely applied as a solvation model for chemical and biological systems. EPISOL is available at https://github.com/EPISOLrelease/EPISOL ." @default.
• W4322718786 created "2023-03-03" @default.
• W4322718786 creator A5054895781 @default.
• W4322718786 creator A5055945646 @default.
• W4322718786 creator A5083071253 @default.
• W4322718786 date "2023-03-01" @default.
• W4322718786 modified "2023-09-26" @default.
• W4322718786 title "<scp>EPISOL</scp>: A software package with expanded functions to perform <scp>3D‐RISM</scp> calculations for the solvation of chemical and biological molecules" @default.
• W4322718786 cites W1487420490 @default.
• W4322718786 cites W1508891349 @default.
• W4322718786 cites W1938874138 @default.
• W4322718786 cites W1964343736 @default.
• W4322718786 cites W1966878558 @default.
• W4322718786 cites W1973358197 @default.
• W4322718786 cites W1978159078 @default.
• W4322718786 cites W1979940130 @default.
• W4322718786 cites W1981818409 @default.
• W4322718786 cites W1984572625 @default.
• W4322718786 cites W1994363288 @default.
• W4322718786 cites W1999273805 @default.
• W4322718786 cites W2001676543 @default.
• W4322718786 cites W2002431986 @default.
• W4322718786 cites W2004233117 @default.
• W4322718786 cites W2004666296 @default.
• W4322718786 cites W2006055880 @default.
• W4322718786 cites W2008505552 @default.
• W4322718786 cites W2010506300 @default.
• W4322718786 cites W2012707472 @default.
• W4322718786 cites W2013810306 @default.
• W4322718786 cites W2015517515 @default.
• W4322718786 cites W2022277441 @default.
• W4322718786 cites W2022984726 @default.
• W4322718786 cites W2025880126 @default.
• W4322718786 cites W2026467865 @default.
• W4322718786 cites W2031152302 @default.
• W4322718786 cites W2035746802 @default.
• W4322718786 cites W2036011280 @default.
• W4322718786 cites W2037176511 @default.
• W4322718786 cites W2040716987 @default.
• W4322718786 cites W2040787539 @default.
• W4322718786 cites W2047150613 @default.
• W4322718786 cites W2048748678 @default.
• W4322718786 cites W2056117284 @default.
• W4322718786 cites W2061018719 @default.
• W4322718786 cites W2064454508 @default.
• W4322718786 cites W2066571741 @default.
• W4322718786 cites W2070038789 @default.
• W4322718786 cites W2073662804 @default.
• W4322718786 cites W2074674539 @default.
• W4322718786 cites W2075494856 @default.
• W4322718786 cites W2079734282 @default.
• W4322718786 cites W2085006242 @default.
• W4322718786 cites W2091213355 @default.
• W4322718786 cites W2095495826 @default.
• W4322718786 cites W2101923653 @default.
• W4322718786 cites W2116748424 @default.
• W4322718786 cites W2121695928 @default.
• W4322718786 cites W2122395553 @default.
• W4322718786 cites W2131754023 @default.
• W4322718786 cites W2143598945 @default.
• W4322718786 cites W2144525471 @default.
• W4322718786 cites W2145310386 @default.
• W4322718786 cites W2160164236 @default.
• W4322718786 cites W2160820192 @default.
• W4322718786 cites W2314316427 @default.
• W4322718786 cites W2322014717 @default.
• W4322718786 cites W2324695576 @default.
• W4322718786 cites W2329171533 @default.
• W4322718786 cites W2378074933 @default.
• W4322718786 cites W2508815757 @default.
• W4322718786 cites W2522835401 @default.
• W4322718786 cites W2547914817 @default.
• W4322718786 cites W2735641011 @default.
• W4322718786 cites W2754217508 @default.
• W4322718786 cites W2762283147 @default.
• W4322718786 cites W2777586635 @default.
• W4322718786 cites W2790828835 @default.
• W4322718786 cites W2901894003 @default.
• W4322718786 cites W2945227468 @default.
• W4322718786 cites W3011118003 @default.
• W4322718786 cites W3044907747 @default.
• W4322718786 cites W4307344335 @default.
• W4322718786 doi "https://doi.org/10.1002/jcc.27088" @default.
• W4322718786 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/36856731" @default.
• W4322718786 hasPublicationYear "2023" @default.
• W4322718786 type Work @default.
• W4322718786 citedByCount "0" @default.
• W4322718786 crossrefType "journal-article" @default.
• W4322718786 hasAuthorship W4322718786A5054895781 @default.
• W4322718786 hasAuthorship W4322718786A5055945646 @default.
• W4322718786 hasAuthorship W4322718786A5083071253 @default.
• W4322718786 hasBestOaLocation W43227187861 @default.
• W4322718786 hasConcept C10803110 @default.
• W4322718786 hasConcept C121332964 @default.
• W4322718786 hasConcept C121864883 @default.
• W4322718786 hasConcept C147597530 @default.
• W4322718786 hasConcept C148093993 @default.
• W4322718786 hasConcept C152365726 @default.

• next