CAVER: A new tool to explore routes from protein clefts, pockets and cavities

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Petřek, Martin ^a   Otyepka, Michal ^b   Banáš, Pavel ^b   Košinová, Pavlína ^b   Koča, Jaroslav ^a   Damborský, Jiří ^a  

^a MASARYK UNIVERSITY   (Czech Republic)

^b PALACKÝ UNIVERSITY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED IDENTIFICATION; CRYSTALLOGRAPHIC ANALYSIS; DISTANCE FUNCTIONS; FUNCTIONAL PROGRAMS; INORGANIC MATERIALS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR DYNAMICS TRAJECTORIES; STAND-ALONE VERSION;

ALGORITHMS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACIDS;

PROTEINS;

ARTICLE; COMPUTER ANALYSIS; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; GENETIC ALGORITHM; MOLECULAR DYNAMICS; MOLECULAR MODEL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; STRUCTURAL PROTEOMICS; ALGORITHM; CHEMISTRY; COMPUTER SIMULATION; INTERNET; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROCEDURES; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEOMICS; RHODOCOCCUS; SOFTWARE; SPHINGOMONAS; X RAY CRYSTALLOGRAPHY; XANTHOBACTER;

PROTEIN; SOLVENT;

ALGORITHMS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; INTERNET; MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; PROTEOMICS; RHODOCOCCUS; SOFTWARE; SOLVENTS; SPHINGOMONAS; XANTHOBACTER;

EID: 33847142225     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-316     Document Type: Article

References (32)

1. Kleywegt GJ Jones TA Detection, delineation, measurement and display of cavities in macromolecular structures Acta Crystallographica Section D 1994 50 178-185
2. Lesk AM Molecular speleology - the exploration of crevices in proteins for prediction of binding-sites, design of drugs and analysis of surface recognition Acta Crystallographica Section A 1986 42 83-85
3. Laurie ATR Jackson RM Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites Bioinformatics 2005 21 1908-1916 10.1093/bioinformatics/bti315 15701681
4. Liang J Edelsbrunner H Woodward C Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design Protein Science 1998 7 1884-1897 9761470
5. Chaloupkova R Sykorova J Prokop Z Jesenska A Monincovaa M Pavlova M Tsuda M Nagata Y Damborsky J Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel Journal of Biological Chemistry 2003 278 52622-52628 10.1074/jbc.M306762200 14525993
6. Bui JM Tai K McCammon JA Acetylcholinesterase: Enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2 Journal of the American Chemical Society 2004 126 7198-7205 10.1021/ ja0485715 15186156
7. Tara S Helms V Straatsma TP McCammon JA Molecular dynamics of mouse acetylcholinesterase complexed with huperzine A Biopolymers 1999 50 347-359 10.1002/ (SICI)1097-0282(19991005)50:4<347::AID-BIP1>3.0.CO;2-R 10423544
8. Bitter I Sato M Bender MA Kaufman A Wan M Wax MR Automatic, accurate and robust colon centerline algorithm Radiology 2000 217 370
9. Bitter I Kaufman AE Sato M Penalized-distance volumetric skeleton algorithm Transactions on Visualization and Computer Graphics 2001 7 195-206 10.1109/2945.942688
10. Wan M Liang ZR Ke Q Hong LC Bitter I Kaufman A Automatic centerline extraction for virtual colonoscopy Transactions on Medical Imaging 2002 21 1450-1460 10.1109/TMI.2002.806409
11. Kaufman AE Lakare S Kreeger K Bitter I Virtual colonoscopy Communications of the ACM 2005 48 37-41 10.1145/1042091.1042117
12. Barber CB Dobkin DP Huhdanpaa H The Quickhull algorithm for convex hulls ACM Transactions on Mathematical Software 1996 22 469-483 10.1145/ 235815.235821
13. Dijkstra EW A note on two problems in connection with graphs Numeriskche Mathematik 1959 1 83-89
14. Ford LR Fulkerson DR Flows in Networks Princeton University Press 1962
15. Bellman R On a Routing Problem Quarterly of Applied Mathematic 1958 16 87-90
16. Floyd RW Algorithm 97: Shortest path Communications of the ACM 1962 5 345 10.1145/367766.368168
17. DeLano WL The case for open-source software in drug discovery Drug Discovery Today 2005 10 213-217 10.1016/S1359-6446(04)03363-X 15708536
18. Damborsky J Rorije E Jesenska A Nagata Y Klopman G Peijnenburg WJGM Structure-specificity relationships for haloalkane dehalogenases Environmental Toxicology and Chemistry 2001 20 2681-2689 10.1897/ 1551-5028(2001)020<2681:SSRFHD>2.0.CO;2
19. Franken SM Rozeboom HJ Kalk KH Dijkstra BW Crystal-structure of haloalkane dehalogenase - an enzyme to detoxify halogenated alkanes EMBO Journal 1991 10 1297-1302 452786 2026135
20. Verschueren KHG Kingma J Rozeboom HJ Kalk KH Janssen DB Dijkstra BW Crystallographic and fluorescence studies of the interaction of haloalkane dehalogenase with halide-ions - studies with halide compounds reveal a halide binding-site in the active-site Biochemistry 1993 32 9031-9037 10.1021/bi00086a008 8369276
21. Verschueren KHG Franken SM Rozeboom HJ Kalk KH Dijkstra BW Refined X-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and implications for the reaction-mechanism Journal of Molecular Biology 1993 232 856-872 10.1006/jmbi.1993.1436 8355275
22. Verschueren KHG Seljee F Rozeboom HJ Kalk KH Dijkstra BW Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase Nature 1993 363 693-698 10.1038/363693a0 8515812
23. Krooshof GH Ridder IS Tepper AWJW Vos GJ Rozeboom HJ Kalk KH Dijkstra BW Janssen DB Kinetic analysis and X-ray structure of haloalkane dehalogenase with a modified halide-binding site Biochemistry 1998 37 15013-15023 10.1021/bi9815187 9790663
24. Pikkemaat MG Ridder IS Rozeboom HJ Kalk KH Dijkstra BW Janssen DB Crystallographic and kinetic evidence of a collision complex formed during halide import in haloalkane dehalogenase Biochemistry 1999 38 12052-12061 10.1021/bi990849w 10508409
25. Ridder IS Rozeboom HJ Dijkstra BW Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15 Angstrom resolution Acta Crystallographica Section D 1999 55 1273-1290
26. Schanstra JP Ridder IS Heimeriks GJ Rink R Poelarends GJ Kalk KH Dijkstra BW Janssen DB Kinetic characterization and X-ray structure of a mutant of haloalkane dehalogenase with higher catalytic activity and modified substrate range Biochemistry 1996 35 13186-13195 10.1021/ bi961151a 8855957
27. Newman J Peat TS Richard R Kan L Swanson PE Affholter JA Holmes IH Schindler JF Unkefer CJ Terwilliger TC Haloalkane dehalogenases: Structure of a Rhodococcus enzyme Biochemistry 1999 38 16105-16114 10.1021/bi9913855 10587433
28. Marek J Vevodova J Smatanova IK Nagata Y Svensson LA Newman J Takagi M Damborsky J Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 Biochemistry 2000 39 14082-14086 10.1021/ bi001539c 11087355
29. Oakley AJ Prokop Z Bohac M Kmunicek J Jedlicka T Monincova M Kuta-Smatanova I Nagata Y Damborsky J Wilce MCJ Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: Evidence for product- and water-mediated inhibition Biochemistry 2002 41 4847-4855 10.1021/bi015734i 11939779
30. Oakley AJ Klvana M Otyepka M Nagata Y Wilce MCJ Damborsky J Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 Angstrom resolution: Dynamics of catalytic residues Biochemistry 2004 43 870-878 14744129
31. Streltsov VA Prokop Z Damborsky J Nagata Y Oakley A Wilce MCJ Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates Biochemistry 2003 42 10104-10112 10.1021/bi027280a 12939138
32. Otyepka M Damborsky J Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains Protein Science 2002 11 1206-1217 10.1110/ps.ps3830102 11967377