Reading List

Suggested Reading from the APBS team

General solvation reviews

APBS parallel multigrid solver

  • Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA, 98, 10037-41, 2001. http://dx.doi.org/10.1073/pnas.181342398

APBS parallel finite element solver

APBS geometric flow solver

  • Chen Z, Baker NA, Wei GW. Differential geometry based solvation model I: Eulerian formulation, J Comput Phys, 229, 8231-58, 2010. http://dx.doi.org/10.1016/j.jcp.2010.06.036
  • Chen Z, Baker NA, Wei GW. Differential geometry based solvation model II: Lagrangian formulation. J Math Biol, 63, 1139-1200, 2011. http://dx.doi.org/10.1007/s00285-011-0402-z
  • Chen Z, Zhao S, Chun J, Thomas DG, Baker NA, Wei GW. Variational approach for nonpolar solvation analysis. Journal of Chemical Physics, 137, 084101, 2012. http://dx.doi.org/10.1063/1.4745084
  • Thomas DG, Chun J, Chen Z, Wei G, Baker NA. Parameterization of a Geometric Flow Implicit Solvation Model. Journal of Computational Chemistry, 34, 687-95, 2013. http://dx.doi.org/10.1002/jcc.23181
  • Daily M, Chun J, Heredia-Langner A, Baker NA. Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies. J Chem Phys, 139, 204108, 2013. http://dx.doi.org/10.1063/1.4832900

Preparing protein structures and calculating pKa values

  • Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res, 32, W665-7, 2004. http://dx.doi.org/10.1093/nar/gkh381
  • Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007. http://dx.doi.org/10.1093/nar/gkm276
  • Carstensen T, Farrell D, Huang Y, Baker NA, Nielsen JE. On the development of protein pKa calculation algorithms. Proteins, 79, 3287-3298, 2011. http://dx.doi.org/10.1002/prot.23091
  • Alexov E, Mehler EL, Baker N, Baptista A, Huang Y, Milletti F, Nielsen JE, Farrell D, Carstensen T, Olsson MHM, Shen JK, Warwicker J, Williams, Word MJ. Progress in the prediction of pKa values in proteins. Proteins, 79, 3260-3275, 2011. http://dx.doi.org/10.1002/prot.23189
  • Gosink LJ, Hogan EA, Pulsipher TC, Baker NA. Bayesian model aggregation for ensemble-based estimates of protein pKa values. Proteins, 82 (3), 354-363, 2014. http://dx.doi.org/10.1002/prot.24390

Structural bioinformatics based on electrostatic properties

  • Zhang X, Bajaj CL, Kwon B, Dolinsky TJ, Nielsen JE, Baker NA. Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity. Multiscale Model Simul, 5, 1196-213, 2006. http://dx.doi.org/10.1137/050647670
  • Chakraborty S, Rao BJ, Baker N, Ásgeirsson B. Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator. Intrinsically Disordered Proteins, 1 (1), e25463, 2013. https://www.landesbioscience.com/journals/idp/article/25463/

Other fun with APBS and PDB2PQR

  • Wagoner JA, Baker NA. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci USA, 103, 8331-6, 2006. http://dx.doi.org/10.1073/pnas.0600118103
  • Swanson JMJ, Wagoner JA, Baker NA, McCammon JA. Optimizing the Poisson dielectric boundary with explicit solvent forces and energies: lessons learned with atom-centered dielectric functions. J Chem Theory Comput, 3, 170-83, 2007. http://dx.doi.org/10.1021/ct600216k
  • Schnieders MJ, Baker NA, Ren P, Ponder JW. Polarizable Atomic Multipole Solutes in a Poisson-Boltzmann Continuum. J Chem Phys, 126, 124114, 2007. http://dx.doi.org/10.1063/1.2714528
  • Callenberg KM, Choudhary OP, de Forest GL, Gohara DW, Baker NA, Grabe M. APBSmem: A graphical interface for electrostatic calculations at the membrane. PLoS ONE, 5, e12722, 2010. http://dx.doi.org/10.1371/journal.pone.0012722
  • Unni S, Huang Y, Hanson RM, Tobias M, Krishnan S, Li WW, Nielsen JE, Baker NA. Web servers and services for electrostatics calculations with APBS and PDB2PQR. J Comput Chem, 32 (7), 1488-1491, 2011. http://dx.doi.org/10.1002/jcc.21720
  • Konecny R, Baker NA, McCammon JA. iAPBS: a programming interface to the adaptive Poisson–Boltzmann solver. Computational Science & Discovery, 5, 015005, 2012. http://dx.doi.org/10.1088/1749-4699/5/1/015005

More papers in electrostatics

  • The APBS team updates this Mendeley page with papers in electrostatics.