72 related articles for article (PubMed ID: 17503352)
1. Computational methods for functional site identification suggest a substrate access channel in transaldolase.
Silberstein M; Landon MR; Wang YE; Perl A; Vajda S
Genome Inform; 2006; 17(1):13-22. PubMed ID: 17503352
[TBL] [Abstract][Full Text] [Related]
2. Exploring the binding site structure of the PPAR gamma ligand-binding domain by computational solvent mapping.
Sheu SH; Kaya T; Waxman DJ; Vajda S
Biochemistry; 2005 Feb; 44(4):1193-209. PubMed ID: 15667213
[TBL] [Abstract][Full Text] [Related]
3. Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450.
Clodfelter KH; Waxman DJ; Vajda S
Biochemistry; 2006 Aug; 45(31):9393-407. PubMed ID: 16878974
[TBL] [Abstract][Full Text] [Related]
4. Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design.
Imai T; Oda K; Kovalenko A; Hirata F; Kidera A
J Am Chem Soc; 2009 Sep; 131(34):12430-40. PubMed ID: 19655800
[TBL] [Abstract][Full Text] [Related]
5. Algorithms for computational solvent mapping of proteins.
Kortvelyesi T; Dennis S; Silberstein M; Brown L; Vajda S
Proteins; 2003 May; 51(3):340-51. PubMed ID: 12696046
[TBL] [Abstract][Full Text] [Related]
6. Crystallographic and functional characterization of the fluorodifen-inducible glutathione transferase from Glycine max reveals an active site topography suited for diphenylether herbicides and a novel L-site.
Axarli I; Dhavala P; Papageorgiou AC; Labrou NE
J Mol Biol; 2009 Jan; 385(3):984-1002. PubMed ID: 19014949
[TBL] [Abstract][Full Text] [Related]
7. Redesigning the active site of transaldolase TalB from Escherichia coli: new variants with improved affinity towards nonphosphorylated substrates.
Schneider S; Gutiérrez M; Sandalova T; Schneider G; Clapés P; Sprenger GA; Samland AK
Chembiochem; 2010 Mar; 11(5):681-90. PubMed ID: 20148428
[TBL] [Abstract][Full Text] [Related]
8. Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures.
Gong S; Blundell TL
PLoS Comput Biol; 2008 Oct; 4(10):e1000179. PubMed ID: 18833291
[TBL] [Abstract][Full Text] [Related]
9. Molecular docking for substrate identification: the short-chain dehydrogenases/reductases.
Favia AD; Nobeli I; Glaser F; Thornton JM
J Mol Biol; 2008 Jan; 375(3):855-74. PubMed ID: 18036612
[TBL] [Abstract][Full Text] [Related]
10. Computed protonation properties: unique capabilities for protein functional site prediction.
Murga LF; Wei Y; Ondrechen MJ
Genome Inform; 2007; 19():107-18. PubMed ID: 18546509
[TBL] [Abstract][Full Text] [Related]
11. Binding response: a descriptor for selecting ligand binding site on protein surfaces.
Zhong S; MacKerell AD
J Chem Inf Model; 2007; 47(6):2303-15. PubMed ID: 17900106
[TBL] [Abstract][Full Text] [Related]
12. From structure to function: insights into the catalytic substrate specificity and thermostability displayed by Bacillus subtilis mannanase BCman.
Yan XX; An XM; Gui LL; Liang DC
J Mol Biol; 2008 Jun; 379(3):535-44. PubMed ID: 18455734
[TBL] [Abstract][Full Text] [Related]
13. Kinetic and structural analysis of mutant Escherichia coli dihydroorotases: a flexible loop stabilizes the transition state.
Lee M; Maher MJ; Christopherson RI; Guss JM
Biochemistry; 2007 Sep; 46(37):10538-50. PubMed ID: 17711307
[TBL] [Abstract][Full Text] [Related]
14. Analysis of CYP2D6 substrate interactions by computational methods.
Ito Y; Kondo H; Goldfarb PS; Lewis DF
J Mol Graph Model; 2008 Feb; 26(6):947-56. PubMed ID: 17764997
[TBL] [Abstract][Full Text] [Related]
15. Structure of the alkalohyperthermophilic Archaeoglobus fulgidus lipase contains a unique C-terminal domain essential for long-chain substrate binding.
Chen CK; Lee GC; Ko TP; Guo RT; Huang LM; Liu HJ; Ho YF; Shaw JF; Wang AH
J Mol Biol; 2009 Jul; 390(4):672-85. PubMed ID: 19447113
[TBL] [Abstract][Full Text] [Related]
16. Model for substrate interactions in C5a peptidase from Streptococcus pyogenes: A 1.9 A crystal structure of the active form of ScpA.
Kagawa TF; O'Connell MR; Mouat P; Paoli M; O'Toole PW; Cooney JC
J Mol Biol; 2009 Feb; 386(3):754-72. PubMed ID: 19152799
[TBL] [Abstract][Full Text] [Related]
17. Deletion of Ser-171 causes inactivation, proteasome-mediated degradation and complete deficiency of human transaldolase.
Grossman CE; Niland B; Stancato C; Verhoeven NM; Van Der Knaap MS; Jakobs C; Brown LM; Vajda S; Banki K; Perl A
Biochem J; 2004 Sep; 382(Pt 2):725-31. PubMed ID: 15115436
[TBL] [Abstract][Full Text] [Related]
18. The crystal structures of ornithine carbamoyltransferase from Mycobacterium tuberculosis and its ternary complex with carbamoyl phosphate and L-norvaline reveal the enzyme's catalytic mechanism.
Sankaranarayanan R; Cherney MM; Cherney LT; Garen CR; Moradian F; James MN
J Mol Biol; 2008 Jan; 375(4):1052-63. PubMed ID: 18062991
[TBL] [Abstract][Full Text] [Related]
19. Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.
Najmanovich R; Kurbatova N; Thornton J
Bioinformatics; 2008 Aug; 24(16):i105-11. PubMed ID: 18689810
[TBL] [Abstract][Full Text] [Related]
20. Redefinition of rubisco carboxylase reaction reveals origin of water for hydration and new roles for active-site residues.
Kannappan B; Gready JE
J Am Chem Soc; 2008 Nov; 130(45):15063-80. PubMed ID: 18855361
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
