DelPhi web server v2: Incorporating atomic-style geometrical figures into the computational protocol

Bioinformatics

Volumn 28, Issue 12, 2012, Pages 1655-1657

  Smith, Nicholas ^a   Witham, Shawn ^a   Sarkar, Subhra ^a,b   Zhang, Jie ^a,b   Li, Lin ^a   Li, Chuan ^a   Alexov, Emil ^a  

^a Department of Physics   (United States)

^b AMRL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NANOMATERIAL;

ALGORITHM; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; COMPUTER INTERFACE; COMPUTER PROGRAM; INTERNET; METHODOLOGY; STATIC ELECTRICITY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; INTERNET; MODELS, MOLECULAR; NANOSTRUCTURES; SOFTWARE; STATIC ELECTRICITY; USER-COMPUTER INTERFACE;

EID: 84863504613     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts200     Document Type: Article

References (10)

1. Alexov, E. (2004) Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and three-dimensional structure. Eur. J. Biochem., 271, 173-185.
2. Alexov, E. et al. (2011) Progress in the prediction of pKa values in proteins. Proteins, 79, 3260-3275.
3. Baker, N.A. and McCammon, J.A. (2003) Electrostatic interactions. Meth. Biochem. Anal., 44, 427-440.
4. Mi, W. et al. (2008) The crystal structure of human chloride intracellular channel protein 2: a disulfide bond with functional implications. Proteins, 71, 509-513.
5. Rocchia, W. et al. (2002) Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J. Comput. Chem., 23, 128-137.
6. Sarkar, S. et al. (2012) DelPhi web server: a comprehensive online suite for electostatic calculations of biological macromolecules and their complexes. Commun. Comput. Phys., (in press).
7. Talley, K. et al. (2008) On the electrostatic component of protein-protein binding free energy. PMC Biophys., 1, 2.
8. Tan, Z.J. and Chen, S.J. (2011) Salt contribution to RNA tertiary structure folding stability. Biophys. J., 101, 176-187.
9. Tang, C.L. et al. (2007) Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. J. Mol. Biol., 366, 1475-1496.
10. Unni, S. et al. (2011)Web servers and services for electrostatics calculations with APBS and PDB2PQR. J. Comput. Chem., 32, 1488-1491.