Literature DB >> 22905037

iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS).

Robert Konecny1, Nathan A Baker, J Andrew McCammon.   

Abstract

The Adaptive Poisson-Boltzmann Solver (APBS) is a state-of-the-art suite for performing Poisson-Boltzmann electrostatic calculations on biomolecules. The iAPBS package provides a modular programmatic interface to the APBS library of electrostatic calculation routines. The iAPBS interface library can be linked with a FORTRAN or C/C++ program thus making all of the APBS functionality available from within the application. Several application modules for popular molecular dynamics simulation packages - Amber, NAMD and CHARMM are distributed with iAPBS allowing users of these packages to perform implicit solvent electrostatic calculations with APBS.

Entities:  

Year:  2012        PMID: 22905037      PMCID: PMC3419494          DOI: 10.1088/1749-4699/5/1/015005

Source DB:  PubMed          Journal:  Comput Sci Discov        ISSN: 1749-4699


  16 in total

1.  Electrostatics of nanosystems: application to microtubules and the ribosome.

Authors:  N A Baker; D Sept; S Joseph; M J Holst; J A McCammon
Journal:  Proc Natl Acad Sci U S A       Date:  2001-08-21       Impact factor: 11.205

2.  Accelerated Poisson-Boltzmann calculations for static and dynamic systems.

Authors:  Ray Luo; Laurent David; Michael K Gilson
Journal:  J Comput Chem       Date:  2002-10       Impact factor: 3.376

3.  PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations.

Authors:  Todd J Dolinsky; Jens E Nielsen; J Andrew McCammon; Nathan A Baker
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

4.  Poisson-Boltzmann methods for biomolecular electrostatics.

Authors:  Nathan A Baker
Journal:  Methods Enzymol       Date:  2004       Impact factor: 1.600

5.  Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:  Lessons Learned with Atom-Centered Dielectric Functions.

Authors:  Jessica M J Swanson; Jason A Wagoner; Nathan A Baker; J A McCammon
Journal:  J Chem Theory Comput       Date:  2007-01       Impact factor: 6.006

6.  Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms.

Authors:  Jason A Wagoner; Nathan A Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2006-05-18       Impact factor: 11.205

Review 7.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

Review 8.  Biomolecular electrostatics and solvation: a computational perspective.

Authors:  Pengyu Ren; Jaehun Chun; Dennis G Thomas; Michael J Schnieders; Marcelo Marucho; Jiajing Zhang; Nathan A Baker
Journal:  Q Rev Biophys       Date:  2012-11       Impact factor: 5.318

Review 9.  Classical electrostatics in biology and chemistry.

Authors:  B Honig; A Nicholls
Journal:  Science       Date:  1995-05-26       Impact factor: 47.728

10.  Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids.

Authors:  Robert Konecny; Joanna Trylska; Florence Tama; Deqiang Zhang; Nathan A Baker; Charles L Brooks; J A McCammon
Journal:  Biopolymers       Date:  2006-06-05       Impact factor: 2.505

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  19 in total

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Authors:  Veronica Kane Dickson; Leanne Pedi; Stephen B Long
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2.  Computer-aided identification of a novel pyruvate kinase M2 activator compound.

Authors:  Yuanyuan Li; Minyue Bao; Chunlan Yang; Jiao Chen; Shu Zhou; Rong Sun; Chuanfang Wu; Xin Li; Jinku Bao
Journal:  Cell Prolif       Date:  2018-08-21       Impact factor: 6.831

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Authors:  Elizabeth Jurrus; Dave Engel; Keith Star; Kyle Monson; Juan Brandi; Lisa E Felberg; David H Brookes; Leighton Wilson; Jiahui Chen; Karina Liles; Minju Chun; Peter Li; David W Gohara; Todd Dolinsky; Robert Konecny; David R Koes; Jens Erik Nielsen; Teresa Head-Gordon; Weihua Geng; Robert Krasny; Guo-Wei Wei; Michael J Holst; J Andrew McCammon; Nathan A Baker
Journal:  Protein Sci       Date:  2017-10-24       Impact factor: 6.725

4.  Progress in developing Poisson-Boltzmann equation solvers.

Authors:  Chuan Li; Lin Li; Marharyta Petukh; Emil Alexov
Journal:  Mol Based Math Biol       Date:  2013-03-01

5.  Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.

Authors:  Brian K Radak; Tai-Sung Lee; Michael E Harris; Darrin M York
Journal:  RNA       Date:  2015-07-13       Impact factor: 4.942

6.  Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules.

Authors:  Lin Li; Joshua Alper; Emil Alexov
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7.  The Interaction of FABP with Kapα.

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8.  Protein signatures using electrostatic molecular surfaces in harmonic space.

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9.  Web-based computational chemistry education with CHARMMing III: Reduction potentials of electron transfer proteins.

Authors:  B Scott Perrin; Benjamin T Miller; Vinushka Schalk; H Lee Woodcock; Bernard R Brooks; Toshiko Ichiye
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10.  Insight on Mutation-Induced Resistance from Molecular Dynamics Simulations of the Native and Mutated CSF-1R and KIT.

Authors:  Priscila Da Silva Figueiredo Celestino Gomes; Isaure Chauvot De Beauchêne; Nicolas Panel; Sophie Lopez; Paulo De Sepulveda; Pedro Geraldo Pascutti; Eric Solary; Luba Tchertanov
Journal:  PLoS One       Date:  2016-07-28       Impact factor: 3.240

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