VASCo: Computation and visualization of annotated protein surface contacts

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Steinkellner, Georg ^a,b   Rader, Robert ^c,d   Thallinger, Gerhard G ^c   Kratky, Christoph ^a   Gruber, Karl ^a,b  

^a UNIVERSITY OF GRAZ   (Austria)

^b RESEARCH CENTRE APPLIED BIOCATALYSIS   (Austria)

^c GRAZ UNIVERSITY OF TECHNOLOGY   (Austria)

^d INSTITUTE FOR MICROELECTRONICS   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

AMOUNT OF INFORMATION; BIOLOGICAL INTERACTIONS; CRYSTALLOGRAPHIC ANALYSIS; ELECTROSTATIC POTENTIALS; MOLECULAR PROPERTIES; PHYSICO-CHEMICAL INTERACTIONS; PROTEIN-PROTEIN INTERACTIONS; VISUALIZATION AND ANALYSIS;

BIOINFORMATICS; DATA VISUALIZATION; MOLECULES; SOFTWARE PACKAGES; SURFACE PROPERTIES; TOOLS; VISUALIZATION;

PROTEINS;

PROTEIN;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; HYDROPHOBICITY; PROTEIN CONFORMATION; PROTEIN DATABASE;

BINDING SITES; DATABASES, PROTEIN; HYDROPHOBICITY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 61649097496     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-32     Document Type: Article

References (52)

1. Berman H Henrick K Nakamura H Markley JL The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data Nucleic Acids Res 2007, 35:D301-D303. 1669775 17142228
2. Berman HM Battistuz T Bhat TN Bluhm WF Bourne PE Burkhardt K Feng Z Gilliland GL Iype L Jain S et al. The Protein Data Bank Acta Crystallogr D Biol Crystallogr 2002, 58:899-907. 12037327
3. Darnell SJ Page D Mitchell JC An automated decision-tree approach to predicting protein interaction hot spots Proteins 2007, 68(4):813-823. 17554779
4. Franzot G Carugo O Computational approaches to protein-protein interaction J Struct Funct Genomics 2003, 4:245-255. 15185965
5. Shazman S Celniker G Haber O Glaser F Mandel-Gutfreund Y Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces Nucleic Acids Res 2007, 35:W526-530. 1933175 17537808
6. Ofran Y Rost B Analysing six types of protein-protein interfaces Journal of Molecular Biology 2003 325 377 387 12488102
7. Russell RB Alber F Aloy P Davis FP Korkin D Pichaud M Topf M Sali A A structural perspective on protein-protein interactions Current Opinion in Structural Biology 2004, 14:313-324. 15193311
8. Wodak SJ Janin J Structural basis of macromolecular recognition Advances in Protein Chemistry 2002, 61:9-73. 12461820
9. Valencia A Pazos F Computational methods for the prediction of protein interactions Current Opinion in Structural Biology 2002, 12:368-373. 12127457
10. Smith GR Sternberg MJE Prediction of protein-protein interactions by docking methods Current Opinion in Structural Biology 2002, 12:28-35. 11839486
11. Jones S Marin A Thornton JM Protein domain interfaces: Characterization and comparison with oligomeric protein interfaces Protein Engineering 2000, 13:77-82. 10708645
12. Jones S Thornton JM Analysis of protein-protein interaction sites using surface patches Journal of Molecular Biology 1997, 272:121-132. 9299342
13. De S Krishnadev O Srinivasan N Rekha N Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different BMC Structural Biology 2005, 5. 1201154 16105176
14. Bahadur RP Chakrabarti P Rodier F Janin J A Dissection of Specific and Non-specific Protein-Protein Interfaces Journal of Molecular Biology 2004, 336:943-955. 15095871
15. Henrick K Thornton JM PQS: A protein quaternary structure file server Trends in Biochemical Sciences 1998, 23:358-361. 9787643
16. Brinda KV Vishveshwara S Oligomeric protein structure networks: Insights into protein-protein interactions BMC Bioinformatics 2005:6. 1326230 16336694
17. The World Index of Molecular Visualization Resource http://www.molvisindex.org/
18. Global Protein Surface Survey http://gpss.mcsg.anl.gov/
19. Mark-Us: A Function Annotation Server http://luna.bioc.columbia.edu/ honiglab/mark-us/
20. Porollo A Meller J Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D BMC bioinformatics 2007, 8:316. 1978507 17727718
21. Weisel M Proschak E Schneider G PocketPicker: Analysis of ligand binding-sites with shape descriptors Chemistry Central Journal 2007:1. 1994066 17880740
22. Teyra J Doms A Schroeder M Pisabarro MT SCOWLP: A web-based database for detailed characterization and visualization of protein interfaces BMC Bioinformatics 2006:7. 1459204 16512892
23. Murzin AG Brenner SE Hubbard T Chothia C SCOP: A structural classification of proteins database for the investigation of sequences and structures Journal of Molecular Biology 1995, 247:536-540. 7723011
24. Jmol: An open-source Java viewer for chemical structures in 3D http://www.jmol.org/
25. Guex N Peitsch MC SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling Electrophoresis 1997, 18:2714-2723. 9504803
26. The PyMOL Molecular Graphics System http://pymol.sourceforge.net/
27. Python Programming Language http://www.python.org/
28. Sanner MF Olson AJ Spehner J-C Reduced surface: An efficient way to compute molecular surfaces Biopolymers 1996, 38:305-320. 8906967
29. Honig B Nicholls A Classical electrostatics in biology and chemistry Science 1995, 268:1144-1149. 7761829
30. Nicholls A Honig B A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation J Comput Chem 1991, 12:435-445.
31. Naccess V2.1.1 - Atomic Solvent Accessible Area Calculations http://www.bioinf.manchester.ac.uk/naccess/
32. Tsodikov OV Thomas Record M Jr Sergeev YV Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature Journal of Computational Chemistry 2002, 23:600-609. 11939594
33. Eisenhaber F Lijnzaad P Argos P Sander C Scharf M The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies J Comput Chem 1995, 16:273-284.
34. Eisenhaber F Argos P Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency J Comp Chem 1993, 14:1272-1280.
35. Connolly ML The molecular surface package Journal of Molecular Graphics 1993, 11:139-141. 8347567
36. Ghose AK Crippen GM Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships. I. Partition coefficients as a measure of hydrophobicity J Comput Chem 1986, 7:565-577.
37. Ghose AK Viswanadhan VN Wendoloski JJ Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules Using Fragmental Methods: An Analysis of ALOGP and CLOGP Methods J Phys Chem A 1998, 102:3762-3772.
38. Viswanadhan VN Ghose AK Revankar GR Robins RK Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics J Chem Inf Comput Sci 1989, 29:163-172.
39. Audry E Dubost JP Colleter JC Dallet P A new approach of structure activity relationships: The 'potential of molecular lipophilicity' European Journal of Medicinal Chemistry 1986, 21:71-72.
40. Heiden W Moeckel G Brickmann J A new approach to analysis and display of local lipophilicity/hydrophilicity mapped on molecular surfaces J Comput Aided Mol Des 1993, 7:503-514. 8294943
41. Zviling M Leonov H Arkin IT Genetic algorithm-based optimization of hydrophobicity tables Bioinformatics 2005, 21:2651-2656. 15797910
42. Pearlman DA Case DA Caldwell JW Ross WS Cheatham TE III DeBolt S Ferguson D Seibel G Kollman P "AMBER", a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to stimulate the structural and energetic properties of molecules Comput Phys Commun 1995, 91:1-42.
43. Giacovazzo C Monaco HL Viterbo D Scordari F Gilli G Zanoti G Catti M Fundamentals of crystallography IUCr Texts on Crystallography No 2 1995:2.
44. The CCP4 suite: Programs for protein crystallography Acta Crystallogr D Biol Crystallogr 1994, 50(Pt 5):760-763. 15299374
45. Verdecia MA Larkin RM Ferrer J-L Riek R Chory J Noel JP Structure of the Mg-chelatase cofactor GUN4 reveals a novel hand-shaped fold for porphyrin binding PLoS Biol 2005, 3:e151. 1084334 15884974
46. Albeck S Dym O Unger T Snapir Z Bercovich Z Kahana C Crystallographic and biochemical studies revealing the structural basis for antizyme inhibitor function Protein Science 2008, 17:793-802. 18369191
47. Kern AD Oliveira MA Coffino P Hackert ML Structure of mammalian ornithine decarboxylase at 1.6 Å resolution: Stereochemical implications of PLP-dependent amino acid decarboxylases Structure 1999, 7:567-581. 10378276
48. Kuglstatter A Oubridge C Nagai K Induced structural changes of 7SL RNA during the assembly of human signal recognition particle Nat Struct Biol 2002, 9:740-744. 12244299
49. Oubridge C Kuglstatter A Jovine L Nagai K Crystal structure of SRP19 in complex with the S domain of SRP RNA and its implication for the assembly of the signal recognition particle Mol Cell 2002, 9:1251-1261. 12086622
50. Hall M Stueckler C Ehammer H Pointner E Oberdorfer G Gruber K Hauer B Stuermer R Kroutil W Macheroux P Faber K Asymmetric bioreduction of C = C bonds using enoate reductases OPR1, OPR3 and YqjM: Enzyme-based stereocontrol Advanced Synthesis and Catalysis 2008, 350:411-418.
51. Breithaupt C Strassner J Breitinger U Huber R Macheroux P Schaller A Clausen T X-ray structure of 12-Oxophytodienoate reductase 1 provides structural insight into substrate binding and specificity within the family of OYE Structure 2001, 9:419-429. 11377202
52. Breithaupt C Kurzbauer R Lilie H Schaller A Strassner J Huber R Macheroux P Clausen T Crystal structure of 12-oxophytodienoate reductase 3 from tomato: Self-inhibition by dimerization Proceedings of the National Academy of Sciences of the United States of America 2006, 103:14337-14342. 1586121 16983071