The Protein-DNA Interface database

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Norambuena, Tomás ^a   Melo, Francisco ^a  

^a PONTIFICIA UNIVERSIDAD CATÓLICA DE CHILE   (Chile)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SPECIFICITIES; DNA-BINDING PROTEIN; ENZYME RECOGNITION; FUNCTIONAL CLASSIFICATION; PROTEIN-DNA COMPLEXES; PROTEIN-DNA INTERFACE; STRUCTURAL INFORMATION; TRANSCRIPTION FACTOR BINDING SITES;

DNA; PROTEINS; X RAY CRYSTALLOGRAPHY;

DATABASE SYSTEMS;

DNA; DNA BINDING PROTEIN;

ARTICLE; BINDING SITE; CHEMISTRY; CLASSIFICATION; NUCLEIC ACID DATABASE; PROTEIN DATABASE; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; DNA; DNA-BINDING PROTEINS;

EID: 77952246173     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-262     Document Type: Article

References (38)

1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000, 28:235-242. 10.1093/nar/28.1.235, 102472, 10592235.
2. Hoffman MM, Khrapov MA, Cox JC, Yao J, Tong L, Ellington AD. AANT: the Amino Acid-Nucleotide Interaction Database. Nucleic Acids Res 2004, 32:D174-D181. 10.1093/nar/gkh128, 308862, 14681388.
3. An J, Nakama T, Kubota Y, Sarai A. 3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules. Bioinformatics 1998, 14:188-195. 10.1093/bioinformatics/14.2.188, 9545451.
4. Prabakaran P, An J, Gromiha MM, Selvaraj S, Uedaira H, Kono H, Sarai A. Thermodynamic database for protein-nucleic acid interactions (ProNIT). Bioinformatics 2001, 17:1027-1034. 10.1093/bioinformatics/17.11.1027, 11724731.
5. Spirin S, Titov M, Karyagina A, Alexeevski A. NPIDB: a database of nucleic acids-protein interactions. Bioinformatics 2007, 23:3247-3248. 10.1093/bioinformatics/btm519, 17977883.
6. Lee S, Blundell TL. BIPA: a database for protein-nucleic acid interaction in 3D structures. Bioinformatics 2009, 25:1559-1560. 10.1093/bioinformatics/btp243, 19357098.
7. Contreras-Moreira B. 3D-footprint: a database for the structural analysis of protein-DNA complexes. Nucleic Acids Res 2010, 38:D91-D97. 10.1093/nar/gkp781, 2808867, 19767616.
8. Luscombe NM, Austin SE, Berman HM, Thornton JM. An overview of the structures of protein-DNA complexes. Genome Biol 2000, 1:REVIEWS001. 10.1186/gb-2000-1-1-reviews001, 138832, 11104519.
9. Prabakaran P, Siebers JG, Ahmad S, Gromiha MM, Singarayan MG, Sarai A. Classification of protein-DNA complexes based on structural descriptors. Structure 2006, 14:1355-1367. 10.1016/j.str.2006.06.018, 16962967.
10. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH--a hierarchic classification of protein domain structures. Structure 1997, 5:1093-1108. 10.1016/S0969-2126(97)00260-8, 9309224.
11. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
12. Suhrer SJ, Wiederstein M, Gruber M, Sippl MJ. COPS--a novel workbench for explorations in fold space. Nucleic Acids Res 2009, 37:W539-W544. 10.1093/nar/gkp411, 2703906, 19465386.
13. Ferrada E, Melo F. Effective knowledge-based potentials. Protein Sci 2009, 18:1469-1485. 10.1002/pro.166, 19530247.
14. Seeman NC, Rosenberg JM, Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci USA 1976, 73:804-808. 10.1073/pnas.73.3.804, 336007, 1062791.
15. Pabo CO, Sauer RT. Protein-DNA recognition. Annu Rev Biochem 1984, 53:293-321. 10.1146/annurev.bi.53.070184.001453, 6236744.
16. Mandel-Gutfreund Y, Schueler O, Margalit H. Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles. J Mol Biol 1995, 253:370-382. 10.1006/jmbi.1995.0559, 7563096.
17. Zhou P, Tian F, Lv F, Shang Z. Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins. Proteins 2009, 76:151-163. 10.1002/prot.22327, 19089987.
18. Mandel-Gutfreund Y, Margalit H, Jernigan RL, Zhurkin VB. A role for CH...O interactions in protein-DNA recognition. J Mol Biol 1998, 277:1129-1140. 10.1006/jmbi.1998.1660, 9571027.
19. Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM. PDBsum: a Web-based database of summaries and analyses of all PDB structures. Trends Biochem Sci 1997, 22:488-490. 10.1016/S0968-0004(97)01140-7, 9433130.
20. Luscombe NM, Laskowski RA, Thornton JM. NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Nucleic Acids Res 1997, 25:4940-4945. 10.1093/nar/25.24.4940, 147160, 9396800.
21. McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J Mol Biol 1994, 238:777-793. 10.1006/jmbi.1994.1334, 8182748.
22. Jmol: an open-source Java viewer for chemical structures in 3D. , http://www.jmol.org/
23. Wintjens R, Liévin J, Rooman M, Buisine E. Contribution of cation-pi interactions to the stability of protein-DNA complexes. J Mol Biol 2000, 302:395-410. 10.1006/jmbi.2000.4040, 10970741.
24. Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. The role of DNA shape in protein-DNA recognition. Nature 2009, 461:1248-1253. 10.1038/nature08473, 2793086, 19865164.
25. Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C. Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature 2008, 452:961-965. 10.1038/nature06889, 2587245, 18432238.
26. Williams RJ. Restriction endonucleases: classification, properties, and applications. Mol Biotechnol 2003, 23:225-243. 10.1385/MB:23:3:225, 12665693.
27. Sam MD, Cascio D, Johnson RC, Clubb RT. Crystal structure of the excisionase-DNA complex from bacteriophage lambda. J Mol Biol 2004, 338:229-240. 10.1016/j.jmb.2004.02.053, 15066428.
28. Larivière L, Sommer N, Moréra S. Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase. J Mol Biol 2005, 352:139-150. 10.1016/j.jmb.2005.07.007, 16081100.
29. Fromme JC, Banerjee A, Verdine GL. DNA glycosylase recognition and catalysis. Curr Opin Struct Biol 2004, 14:43-49. 10.1016/j.sbi.2004.01.003, 15102448.
30. Lee JY, Yang W. UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke. Cell 2006, 127:1349-1360. 10.1016/j.cell.2006.10.049, 1866287, 17190599.
31. Nandakumar J, Nair PA, Shuman S. Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate. Mol Cell 2007, 26:257-271. 10.1016/j.molcel.2007.02.026, 17466627.
32. Brenner C, Fuks F. DNA methyltransferases: facts, clues, mysteries. Curr Top Microbiol Immunol 2006, 301:45-66. full_text, 16570845.
33. Mees A, Klar T, Gnau P, Hennecke U, Eker AP, Carell T, Essen LO. Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair. Science 2004, 306:1789-1793. 10.1126/science.1101598, 15576622.
34. Brautigam CA, Steitz TA. Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr Opin Struct Biol 1998, 8:54-63. 10.1016/S0959-440X(98)80010-9, 9519297.
35. Guo F, Gopaul DN, van Duyne GD. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature 1997, 389:40-46. 10.1038/37925, 9288963.
36. Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol WG. Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science 1998, 279:1504-1513. 10.1126/science.279.5356.1504, 9488644.
37. Löwe J, Ellonen A, Allen MD, Atkinson C, Sherratt DJ, Grainge I. Molecular mechanism of sequence-directed DNA loading and translocation by FtsK. Mol Cell 2008, 31:498-509. 10.1016/j.molcel.2008.05.027, 2570039, 18722176.
38. Davies DR, Goryshin IY, Reznikoff WS, Rayment I. Three-dimensional structure of the Tn5 synaptic complex transposition intermediate. Science 2000, 289:77-85. 10.1126/science.289.5476.77, 10884228.