Free Energy References
This is a list of free energy categories. Select the category, and add any references. You will need to log in (create an account) to be able to add to this page, but otherwise it is publicly editable.
To add a reference, and list authors, titles, and journal information. Papers that have not yet appeared in print editions are fine, as long as you can provide a link to an online version of the article through the journal site. As far as possible please follow the formatting of existing references.
To name the paper uniquely, name it {FirstAuthorName}{JournalAbbreviation}{Year}{letter} where the 'letter' is a,b,c, and so forth, noting duplicates. So M. R. Shirts and V. S. Pande, J. Chem. Phys. from 2005 becomes MRShirtsJChemPhys2005a.
If you are not sure of the journal abbreviation, you can look it up here
Category:Solvation Free Energy Calculations
Category:Binding Free Energy Calculations
2007
- JWestergrenJPhysChemB2007a Jan Westergren, Lennart Lindfors, Tobias Höglund, Kai Lüder, Sture Nordholm, and Roland Kjellander. "In Silico Prediction of Drug Solubility: 1. Free Energy of Hydration". J. Phys. Chem. B. ASAP article (2007). Abstract
- KLuderJPhysChemB2007a Kai Lüder, Lennart Lindfors, Jan Westergren, Sture Nordholm, and Roland Kjellander. "In Silico Prediction of Drug Solubility: 2. Free Energy of Solvation in Pure Melts". J. Phys. Chem. B. ASAP article (2007). Abstract
- JChangJPhysChemB2007a Jaeeon Chang, Abraham Lenhoff, and Stanley I. Sandler. "Solvation free energy of amino acids and side-chain analogues", J. Phys. Chem. B. ASAP article (2007). Abstract
- BZagrovicJChemTheoComput2007a Bojan Zagrovic and Wilfred F. van Gunsteren. "Computational Analysis of the Mechanism and Thermodynamics of Inhibition of Phosphodiesterase 5A by Synthetic Ligands". JCTC 3, 301-311 (2007). Abstract
2006
- David L. Mobley, John D. Chodera, and Ken A. Dill. "On the use of orientational restraints and symmetry corrections in alchemical free energy calculations". J. Chem. Phys. 125, 084902 (2006). Abstract.
- Guha Jayachandra, Michael R. Shirts, Sanghyun Park and Vijay S. Pande. "Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics". J. Chem. Phys. 125, 084901 (2006). Abstract.
2005
- Philip W. Fowler, Shantenu Jha and Peter V. Coveney. "Grid-based steered thermodynamic integration accelerates the calculation of binding free energies". Phil. Trans. R. Soc. A (2005) 363, 1999–2015. Abstract
- Christophe Chipot, Xavier Rozanska, and Surjit B. Dixit. "Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein". Journal of Computer-Aided Molecular Design (2005) 19: 765–770. Abstract