Closing the side-chain gap in protein loop modeling

Journal of Computer-Aided Molecular Design

Volumn 23, Issue 7, 2009, Pages 411-418

  Rossi, Karen A ^a   Nayeem, Akbar ^a   Weigelt, Carolyn A ^a   Krystek, Stanley R ^a  

^a BRISTOL MYERS SQUIBB   (United States)

Author keywords

Homology modeling; Side chain sampling; Structure based drug design

Indexed keywords

CHAINS; KNOWLEDGE BASED SYSTEMS; PROTEINS; STRUCTURAL DESIGN;

CHAIN CONFORMATIONS; HOMOLOGY MODELING; KEY ISSUES; LOOP CONFORMATION; LOOP MODELS; PROTEIN MODELS; RESAMPLING; SIDE-CHAIN SAMPLING; SIDE-CHAINS; STRUCTURE BASED DRUG DESIGNS;

CONFORMATIONS;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CONFORMATIONAL TRANSITION; DRUG DESIGN; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN STRUCTURE; STRUCTURAL HOMOLOGY;

EID: 67649827410     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-009-9274-3     Document Type: Article

References (24)

1. Nayeem A, Sitkoff D, Krystek S Jr (2006) Protein Sci 15(4):808. doi: 10.1110/ps.051892906
2. Diller DJ, Li R (2003) J Med Chem 46(22):4638. doi: 10.1021/jm020503a
3. Rockey WM, Elcock AH (2006) Curr Protein Pept Sci 7(5):437. doi: 10.2174/ 138920306778559368
4. Engel S, Skoumbourdis AP, Childress J, Neumann S, Deschamps JR, Thomas CJ, Colson AO, Costanzi S, Gershengorn MC (2008) J Am Chem Soc 130(15):5115. doi: 10.1021/ja077620l
5. Evers A, Klabunde T (2005) J Med Chem 48(4):1088. doi: 10.1021/jm0491804
6. Evers A, Klebe G (2004) J Med Chem 47(22):5381. doi: 10.1021/jm0311487
7. Radestock S, Weil T, Renner S (2008) J Chem Inf Model 48(5):1104. doi: 10.1021/ci8000265
8. Cozzetto D, Kryshtafovych A, Ceriani M, Tramontano A (2007) Proteins 69(Suppl. 8):175. doi: 10.1002/prot.21669
9. Moult J, Fidelis K, Kryshtafovych A, Rost B, Hubbard T, Tramontano A (2007) Proteins 69(Suppl. 8):3. doi: 10.1002/prot.21767
10. Tramontano A, Morea V (2003) Proteins 53(Suppl. 6):352. doi: 10.1002/ prot.10543
11. Greer J (1991) Methods Enzymol 202:239. doi: 10.1016/0076-6879(91)02014-Z
12. Rossi KA, Weigelt CA, Nayeem A, Krystek SR Jr (2007) Protein Sci 16(9):1999. doi: 10.1110/ps.072887807
13. Fiser A, Do RKG, Sali A (2000) Protein Sci 9(9):1753. doi: 10.1110/ ps.9.9.1753
14. Jacobson MP, Pincus DL, Rapp CS, Day TJF, Honig B, Shaw DE, Friesner RA (2004) Proteins 55(2):351. doi: 10.1002/prot.10613
15. Spassov VZ, Yan L, Flook PK (2007) Protein Sci 16(3):494. doi: 10.1110/ ps.062447107
16. Momany FA, Rone R (1992) J Comput Chem 13:888. doi: 10.1002/jcc.540130714
17. Smith RE, Lovell SC, Burke DF, Montalvao RW, Blundell TL (2007) Bioinformatics 23(9):1099. doi: 10.1093/bioinformatics/btm073
18. Abagyan R, Totrov M (1994) J Mol Biol 235(3):983. doi: 10.1006/ jmbi.1994.1052
19. Totrov M, Abagyan R (1996) J Struct Biol 116(1):138. doi: 10.1006/ jsbi.1996.0022
20. Xiang Z, Soto CS, Honig B (2002) Proc Natl Acad Sci USA 99(11):7432. doi: 10.1073/pnas.102179699
21. Zhu K, Shirts, Friesner RA (2007) J Chem Theory Comput 3(6):2108-2119. doi: 10.1021/ct700166f
22. Rao S, Sanschagrin PC, Greenwood JR, Repasky MP, Sherman W, Farid R (2008) J Comput Aided Mol Des 22(9):621. doi: 10.1007/s10822-008-9182-y
23. Kim J, Park JG, Chong Y (2007) Mol Simul 33(8):667. doi: 10.1080/ 08927020701297401
24. Huang SY, Zou X (2007) Proteins 66(2):399. doi: 10.1002/prot.21214