HOLLOW: Generating accurate representations of channel and interior surfaces in molecular structures

BMC Structural Biology

Volumn 8, Issue , 2008, Pages

  Ho, Bosco K ^a   Gruswitz, Franz ^b  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENVELOPE PROTEIN; MYOGLOBIN;

ACCURACY; ARTICLE; COMPUTER PROGRAM; CRYSTAL STRUCTURE; CYTOPLASM; PROTEIN STRUCTURE; CHEMICAL STRUCTURE; COMPUTER GRAPHICS; PROTEIN CONFORMATION; SURFACE PROPERTY;

COMPUTER GRAPHICS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; SOFTWARE; SURFACE PROPERTIES;

EID: 57649229060     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-8-49     Document Type: Article

References (13)

1. HOLE: A program for the analysis of the pore dimensions of ion channel structural models. OS Smart JG Neduvelil X Wang BA Wallace MSP Sansom, J Mol Graph Model 1996 14 6 354 10.1016/S0263-7855(97)00009-X
2. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. M Petrek M Otyepka P Banas P Kosinova J Koca J Damborsky, BMC Bioinformatics 2006 7 316 16792811 10.1186/1471-2105-7-316
3. MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels. M Petrek P Kosinova J Koca M Otyepka, Structure 2007 15 11 1357 1363 10.1016/j.str.2007.10.007 17997961
4. The PyMOL Molecular Graphics System. WL DeLano, Palo Alto, Ca, USA.: DeLano Scientific 2002
5. Environment and Exposure to Solvent of Protein Atoms - Lysozyme and Insulin. A Shrake JA Rupley, J Mol Biol 1973 79 2 351 371 10.1016/0022-2836(73) 90011-9 4760134
6. Transport Mechanism of the Nitrosomonas europaea Rhesus Channel Rh50. F Gruswitz CM Ho M del Rosario CM Westhoff RM Stroud, 2008 19031011
7. Detection, Delineation, Measurement and Display of Cavities in Macromolecular Structures. GJ Kleywegt TA Jones, Acta Crystallogr D 1994 50 178 185 10.1107/S0907444993011333 15299456
8. SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. RA Laskowski, J Mol Graph 1995 13 5 323 330 10.1016/0263-7855(95)00073-9 8603061
9. Analytical Molecular-Surface Calculation. ML Connolly, J Appl Crystallogr 1983 16 Oct 548 558 10.1107/S0021889883010985
10. An X-Ray Study of Azide Methaemoglobin. MF Perutz FS Mathews, J Mol Biol 1966 21 1 199 10.1016/0022-2836(66)90088-X 5969763
11. APBS plugin for PyMOL. MG Lerner HA Carlson, Ann Arbor: University of Michigan 2008
12. Electrostatics of nanosystems: application to microtubules and the ribosome. NA Baker D Sept S Joseph MJ Holst JA McCammon, Proc Natl Acad Sci USA 2001 98 18 10037 10041 11517324 10.1073/pnas.181342398
13. Psyco. A Rigo, 2007 http://psyco.sourceforge.net/