12.07.2015 Views

From Protein Structure to Function with Bioinformatics.pdf

From Protein Structure to Function with Bioinformatics.pdf

From Protein Structure to Function with Bioinformatics.pdf

SHOW MORE
SHOW LESS

You also want an ePaper? Increase the reach of your titles

YUMPU automatically turns print PDFs into web optimized ePapers that Google loves.

1 Ab Initio <strong>Protein</strong> <strong>Structure</strong> Prediction 25Wu S, Skolnick J, Zhang Y (2007) Ab initio modeling of small proteins by iterative TASSERsimulations. BMC Biol 5:17Zagrovic B, Snow CD, Shirts MR, et al. (2002) Simulation of folding of a small alpha-helicalprotein in a<strong>to</strong>mistic detail using worldwide-distributed computing. J Mol Biol323(5):927–937Zhang C, Kim SH (2000) Environment-dependent residue contact energies for proteins. Proc NatlAcad Sci USA 97(6):2550–2555Zhang C, Liu S, Zhou H, et al. (2004) An accurate, residue-level, pair potential of mean force forfolding and binding based on the distance-scaled, ideal-gas reference state. <strong>Protein</strong> Sci13(2):400–411Zhang Y (2007) Template-based modeling and free modeling by I-TASSER in CASP7. <strong>Protein</strong>s69(Suppl 8):108–117Zhang Y (2008) Progress and challenges in protein structure prediction. Curr Opin Struct Biol18(3):342–348Zhang Y, Skolnick J (2004a) Au<strong>to</strong>mated structure prediction of weakly homologous proteins on agenomic scale. Proc Natl Acad Sci U S A 101:7594–7599Zhang Y, Skolnick J (2004b) Scoring function for au<strong>to</strong>mated assessment of protein structure templatequality. <strong>Protein</strong>s 57:702–710Zhang Y, Skolnick J (2004c) SPICKER: a clustering approach <strong>to</strong> identify near-native proteinfolds. J Comput Chem 25(6):865–871Zhang Y, Skolnick J (2005a) The protein structure prediction problem could be solved using thecurrent PDB library. Proc Natl Acad Sci USA 102:1029–1034Zhang Y, Skolnick J (2005b) TM-align: a protein structure alignment algorithm based on the TMscore.Nucleic Acids Res 33(7):2302–2309Zhang Y, Kihara D, Skolnick J (2002) Local energy landscape flattening: parallel hyperbolicMonte Carlo sampling of protein folding. <strong>Protein</strong>s 48(2):192–201Zhang Y, Kolinski A, Skolnick J (2003) TOUCHSTONE II: a new approach <strong>to</strong> ab initio proteinstructure prediction. Biophys J 85(2):1145–1164Zhang Y, Hubner I, Arakaki A, et al. (2006) On the origin and completeness of highly likely singledomain protein structures. Proc Natl Acad Sci USA 103:2605–2610Zhou H, Skolnick J (2007) Ab initio protein structure prediction using chunk-TASSER. BiophysJ 93(5):1510–1518Zhou H, Zhou Y (2002) Distance-scaled, finite ideal-gas reference state improves structurederivedpotentials of mean force for structure selection and stability prediction. <strong>Protein</strong> Sci11(11):2714–2726Zhou H, Zhou Y (2005) Fold recognition by combining sequence profiles derived from evolutionand from depth-dependent structural alignment of fragments. <strong>Protein</strong>s 58(2):321–328

Hooray! Your file is uploaded and ready to be published.

Saved successfully!

Ooh no, something went wrong!