Homology Modeling

Structural Bioinformatics

Volumn , Issue , 2005, Pages 509-523

  Krieger, Elmar ^a   Nabuurs, Sander B ^a   Vriend, Gert ^a  

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

Author keywords

Ab initio folding; Homology modeling; Threading

Indexed keywords

AB INITIO; HOMOLOGY MODELING; THREADING;

EID: 84915824986     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/0471721204.ch25     Document Type: Chapter

References (40)

1. Gregoret LM, Cohen FE (1990): Novel method for the rapid evaluation of packing in protein structures. J Mol Biol 211:959-74.
2. Holm L, Sander C (1992): Evaluation of protein models by atomic solvation preference. J Mol Biol 225:93-105.
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990): Basic local alignment search tool. J Mol Biol 215:403-10.
4. Bates PA, Sternberg MJE (1999): Model building by comparison at CASP3: using expert knowledge and computer automation. Proteins (Suppl. 3):47-54.
5. Baumann G, Frommel C, Sander C (1989): Polarity as a criterion in protein design. Protein Eng 2:329-34.
6. Chinea G, Padron G, Hooft RWW, Sander C, Vriend G (1995): The use of position specific rotamers in model building by homology. Proteins 23:415-21.
7. Chothia C, Lesk AM (1986): The relation between the divergence of sequence and structure in proteins. EMBO J 5:823-36.
8. Czaplewski C, Rodziewicz-Motowidlo S, Liwo A, Ripoll DR, Wawak RJ, Scheraga HA (2000):Molecular simulation study of cooperativity in hydrophobic association. Protein Sci 9:1235-45.
9. Dayringer HE, Tramontano A, Fletterick RJ (1986): Interactive program for visualization and modelling of proteins, nucleic acids and small molecules. J Mol Graph 4:82-7.
10. de Filippis V, Sander C, Vriend G (1994): Predicting local structural changes that result from point mutations. Protein Eng 7:1203-8.
11. Desmet J, De Maeyer M, Hazes B, Lasters I (1992): The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356:539-42.
12. Dodge C, Schneider R, Sander C (1998): The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Res 26:313-5.
13. Dunbrack RL Jr, Karplus M (1994): Conformational analysis of the backbone dependent rotamer preferences of protein side chains. Nat Struct Biol 5:334-40.
14. Epstein CJ, Goldberger RF, Anfinsen CB (1963): The genetic control of tertiary protein structure: studies with model systems. Cold Spring Harb Symp Quant Biol 28:439.
15. Fischer D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, Karplus KJ, Kelley LA, Mac-Callum RM, Pawowski K, Rost B, Rychlewski L, Sternberg MJE (1999): CAFASP1: Critical assessment of fully automated structure prediction methods. Proteins (Suppl. 3):209-17.
16. Fiser A, Do RK, Šali A (2000): Modeling of loops in protein structures. Protein Sci 9:1753-73.
17. Hooft RWW, Vriend G, Sander C, Abola EE (1996): Errors in protein structures. Nature 381:272.
18. IBM Blue Gene team (2001): Blue Gene: a vision for protein science using a petaflop supercomputer. IBM Sys J 40:310-27.
19. Krieger E, Koraimann G, Vriend G (2002): Increasing the precision of comparative models with YASARA NOVA-a self-parameterizing force field. Proteins 47:393-402.
20. Liu H, Elstner M, Kaxiras E, Frauenheim T, Hermans J, Yang W (2001): Quantum mechanics simulation of protein dynamics on long timescale. Proteins 44:484-9.
21. Morris AL, MacArthur MW, Hutchinson EG, Thorton JM (1992): Stereochemical quality of protein structure coordinates. Proteins 12:345-64.
22. Novotny J, Rashin AA, Bruccoleri RE (1988): Criteria that discriminate between native proteins and incorrectly folded models. Proteins 4:19-30.
23. Pearson WR (1990): Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 183:63-98.
24. Peitsch MC, Schwede T, Guex N (2000): Automated protein modelling-the proteome in 3D. Pharmacogenomics 1:257-66.
25. Rost B (1999): Twilight zone of protein sequence alignments. Protein Eng 12:85-94.
26. Šali A, Blundell TL (1993): Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779-815.
27. Sanchez R, Šali A (1997): Evaluation of comparative protein structure modeling by MODELLER-3. Proteins (Suppl. 1):50-8.
28. Sanchez R, Šali A (1999): ModBase: a database of comparative protein structure models. Bioinformatics 15:1060-1.
29. Sander C, Schneider R (1991): Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9:56-68.
30. Simons KT, Bonneau R, Ruczinski I, Baker D (1999): Ab initio structure prediction of CASP III targets using ROSETTA. Proteins (Suppl. 3):171-6.
31. Sippl MJ (1990): Calculation of conformational ensembles from potentials of mean force. J Mol Biol 213:859-83.
32. Sippl MJ (1993): Recognition of errors in three dimensional structures of proteins. Proteins 17:355-62.
33. Stites WE, Meeker AK, Shortle D (1994): Evidence for strained interactions between side-chains and the polypeptide backbone. J Mol Biol 235:27-32.
34. Tappura K (2001): Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations. Proteins 44:167-79.
35. Taylor WR (1986): Identification of protein sequence homology by consensus template alignment. J Mol Biol 188:233-58.
36. Thompson JD, Higgins DG, Gibson TJ (1994): ClustalW: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-80.
37. Vriend G (1990): WHAT IF-A molecular modeling and drug design program. J Molec Graphics 8:52-6.
38. Vriend G, Sander C (1993): Quality control of protein models: directional atomic contact analysis. J Applied Crystallogr 26:47-60.
39. Wang J, Cieplak P, Kollman PA (2000): How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21:1049-74.
40. Xiang Z, Honig B (2001): Extending the accuracy limits of prediction for side-chain conformations. J Mol Biol 311:421-30.