Computational Chemistry & Molecular Modeling Group
Cisneros GA, Elking D, Piquemal JP, Darden TA. Numerical fitting of molecular properties to Hermite Gaussians. The journal of physical chemistry. A 2007 111(47):12049-12056. [Abstract](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17973464)
Gorokhov A, Negishi M, Johnson EF, Pedersen LC, Perera L, Darden TA. Explicit Water near the catalytic I-helix Thr in the predicted solution structure of CYP2A4. Biophys J. 2003 84:57-68. [Abstract](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12524265)
Venkateswarlu D, Duke RE, Perera L, Darden TA, Pedersen LG. An all-atom solution-equilibrated model for human extrinsic blood coagulation complex (sTF-VIIa-Xa): a protein docking and molecular dynamics refinement study. J. Throm. Haem. 2003 1:2577-88. [Abstract](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14750502)
Sagui C., Pedersen LG, Darden TA. Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations. J. Chem. Phys. 2004 120:73-87. [Abstract](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15267263)
Herce DH, Perera L, Darden TA, Sagui C. Surface solvation for an ion in a water cluster. J. Chem. Phys. 2005 122(2), 024513. [Abstract](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15638604)
Piquemal JP, Cisneros GA, Reinhardt P, Gresh N, Darden TA. Towards a force field based on density fitting. J. Chem. Phys. 2006 124(10): 104101. [Abstract](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16542062)
Cisneros GA, Piquemal JP, Darden TA. Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions. J. Phys. Chem. 2006 B 110 (28): 13682-13684. [Abstract](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16836309)
Lin P, Wang WT, Pedersen LC, Negishi M, Pedersen LG. Searching for the minimum energy path in the sulfuryl transfer reaction catalyzed by human estrogen sulfotransferase: the role of enzyme dynamics. Inter. J. Quantum. Chem. 2006 106:2981-98.
Piquemal JP, Perera L, Cisneros GA, Ren PY, Pedersen LG, Darden TA. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. 2006 J. Chem. Phys. 125: 054511. [Abstract](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16942230)
Lin P, Pedersen LC, Batra VK, Beard WA, Wilson SH, Pedersen LG. Energy Analysis of chemistry for correct insertion by DNA polymerase beta. Proc. Nat. Acad. Sci. 2006 103:13294-99. [Abstract](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16938895)
Cisneros GA, Piquemal JP, Darden TA. Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods. J. Chem. Phys. 2006 125(18): 184101. [Abstract](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17115732)
Babin V, Roland C, Darden TA, Sagui C. The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections. J. Chem. Phys. 2006 125(20): 204909. [Abstract](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17144742)
Alhamadsheh MM, Gupta S, Hudson RA, Perera L, Tillekeratne LMV. Total synthesis and selective activity of a new class of conformationally-restrained epothilone. Chemistry 2008 14(2):570-581. [Abstract](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17955508)
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