Molecular modeling of protein function regions

Proteins: Structure, Function and Genetics

Volumn 55, Issue 4, 2004, Pages 942-961

  DeWeese Scott, Carol ^a   Moult, John ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

Author keywords

CASP; Comparative modeling; Ligand binding; Protein structure prediction; Structural genomics

Indexed keywords

ANALYTIC METHOD; ARTICLE; LIGAND BINDING; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS;

ALPHA-GLOBULINS; ANIMALS; BINDING SITES; CARBOXYPEPTIDASES; GLUTATHIONE TRANSFERASE; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEOSIDE-DIPHOSPHATE KINASE; PROTEINS; RATS; RECEPTORS, RETINOIC ACID; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 2542543509     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10519     Document Type: Article

References (29)

1. Moult J, Fidelis K, Zemla A, Hubbard T. Critical assessment of methods of protein structure prediction (CASP)-round V. Proteins 2003;53 Suppl 6:334-339.
2. Al-Lazikani B, et al. Protein structure prediction. Curr Opin Chem Biol 2001;5:51-56.
3. Moult J. Predicting protein three-dimensional structure. Curr Opin Biotechnol 1999;10:583-588.
4. Rost B, Sander C. Bridging the protein sequence-structure gap by structure predictions. Annu Rev Biophys Biomol Struct 1996;25: 113-136.
5. Murzin A, Hubbard TJ. Prediction targets of CASP4. Proteins 2001;Suppl 5:8-12.
6. Sippl MJ, et al. Assessment of the CASP4 fold recognition category. Proteins 2001;Suppl 5:55-67.
7. Avbelj F, et al. Molecular dynamics study of the structure and dynamics of a protein molecule in a crystalline ionic environment, Streptomyces griseus protease A. Biochemistry 1990;29:8658-8676.
8. Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998;11:739-747.
9. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
10. Martin AC, MacArthur MW, Thornton JM. Assessment of comparative modeling in CASP2. Proteins 1997;Suppl 1:14-28.
11. Mosimann S, Meleshko R, James MN. A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins 1995;23:301-317.
12. Samudrala R, et al. Confronting the problem of interconnected structural changes in the comparative modeling of proteins. Proteins 1995:23:327-336.
13. Ji X, et al. Structure and function of the xenobiotic substrate binding site of a glutathione S-transferase as revealed by X-ray crystallographic analysis of product complexes with the diastereomers of 9-(S-glutathionyl)-10-hydroxy-9,10-dihydrophenanthrene. Biochemistry 1994;33:1043-1052.
14. Dumas C, et al. X-ray structure of nucleoside diphosphate kinase. Embo J 1992;11:3203-3208.
15. Bocskei Z, et al. Pheromone binding to two rodent urinary proteins revealed by X-ray crystallography. Nature 1992;360:186-188.
16. Lehman-McKeeman LD, et al. 2-sec-butyl-4,5-dihydrothiazole is a ligand for mouse urinary protein and rat alpha 2u-globulin: physiological and toxicological relevance. Toxicol Appl Pharmacol 1998;149:32-40.
17. Lehman-McKeeman LD, Caudill D. Alpha 2u-globulin is the only member of the lipocalin protein superfamily that binds to hyaline droplet inducing agents. Toxicol Appl Pharmacol 1992;116:170-176.
18. Borghoff SJ, Short BG, Swenberg JA. Biochemical mechanisms and pathobiology of alpha 2u-globulin nephropathy. Annu Rev Pharmacol Toxicol 1990;30:349-367.
19. Chaudhuri BN, et al. The structures of alpha 2u-globulin and its complex with a hyaline droplet inducer. Acta Crystallogr D Biol Crystallogr 1999;55(Pt 4):753-762.
20. Kleywegt GJ, Jones TA. Detection, delination, measurement and display of cavities in macromolecular structures. Acta Crystallogr D Biol Crystallogr 1994;50:178-185.
21. Zanotti G, et al. Three-dimensional structure of recombinant human muscle fatty acid-binding protein. J Biol Chem 1992;267: 18541-18550.
22. Kidd RD, et al. A weak calcium binding site in subtilisin BPN' has a dramatic effect on protein stability. J Am Chem Soc 1996;118: 1645-1651.
23. Marti-Renom MA, et al. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000;29: 291-325.
24. Chung SY, Subbiah S. The use of side-chain packing methods in modeling bacteriophage repressor and cro proteins. Protein Sci 1995;4:2300-2309.
25. Tramontano A, Leplae R, Morea V. Analysis and assessment of comparative modeling predictions in CASP4. Proteins 2001;Suppl 5:22-38.
26. Morera S. et al. X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution. Structure 1995;3:1307-1314.
27. Kraulis P. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallog 1991;24: 32-40.
28. Kleywegt GJ, et al. Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid. Structure 1994;2:1241-1258.
29. Wlodawer A, et al. Carboxyl proteinase from Pseudomonas defines a novel family of subtilisin-like enzymes. Nat Struct Biol 2001;8: 442-446.