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.

22 J. Lee et al.Hsieh MJ, Luo R (2004) Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction. <strong>Protein</strong>s 56(3):475–486Im W, Lee MS, Brooks CL (2003) Generalized born model <strong>with</strong> a simple smoothing function. JComput Chem 24(14):1691–1702Jaroszewski L, Rychlewski L, Li Z, et al. (2005) FFAS03: a server for profile–profile sequencealignments. Nucleic Acids Res 33(Web Server issue):W284–288Jauch R, Yeo HC, Kolatkar PR, et al. (2007) Assessment of CASP7 structure predictions for templatefree targets. <strong>Protein</strong>s 69(Suppl 8):57–67Jonassen I, Klose D, Taylor WR (2006) <strong>Protein</strong> model refinement using structural fragment tessellation.Comput Biol Chem 30(5):360–366Jones DT (1999) GenTHREADER: an efficient and reliable protein fold recognition method forgenomic sequences. J Mol Biol 287(4):797–815Jorgensen WL, Tirado-Rives J (1988) The OPLS potential functions for proteins. Energy minimizationsfor crystals of cyclic peptides and crambin. J Am Chem Soc (110):1657–1666Jorgensen WL, Chandrasekhar J, Madura JD, et al. (1983) Comparison of simple potential functionsfor simulating liquid water. J Chem Phys 79:926–935Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS All-A<strong>to</strong>m Force Field on conformational energetics and properties of organic liquids. J Am ChemSoc 118:11225–11236Kaminski GA, Friesner RA, Tirado-Rives J, et al. (2001) Evaluation and Reparametrization of theOPLS-AA Force Field for proteins via comparison <strong>with</strong> accurate quantum chemical calculationson peptides. J Phys Chem B 105:6474–6487Karplus K, Barrett C, Hughey R (1998) Hidden Markov models for detecting remote proteinhomologies. <strong>Bioinformatics</strong> 14:846–856Kihara D, Lu H, Kolinski A, et al. (2001) TOUCHSTONE: an ab initio protein structure predictionmethod that uses threading-based tertiary restraints. Proc Natl Acad Sci USA98(18):10125–10130Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Optimization by simulated annealing. Science220(4598):671–680Klepeis JL, Floudas CA (2003) ASTRO-FOLD: a combina<strong>to</strong>rial and global optimization frameworkfor Ab initio prediction of three-dimensional structures of proteins from the amino acidsequence. Biophys J 85(4):2119–2146Klepeis JL, Wei Y, Hecht MH, et al. (2005) Ab initio prediction of the three-dimensional structureof a de novo designed protein: a double-blind case study. <strong>Protein</strong>s 58(3):560–570Kocher JP, Rooman MJ, Wodak SJ (1994) Fac<strong>to</strong>rs influencing the ability of knowledge-basedpotentials <strong>to</strong> identify native sequence-structure matches. J Mol Biol 235(5):1598–1613Lazaridis T, Karplus M (1999a) Discrimination of the native from misfolded protein models <strong>with</strong>an energy function including implicit solvation. J Mol Biol 288(3):477–487Lazaridis T, Karplus M (1999b) Effective energy function for proteins in solution. <strong>Protein</strong>s35(2):133–152Lee J (1993) New Monte Carlo algorithm: entropic sampling. Phys Rev Lett 71(2):211–214Lee J, Scheraga HA, Rackovsky S (1998) Conformational analysis of the 20-residue membraneboundportion of melittin by conformational space annealing. Biopolymers 46(2):103–116Lee J, Kim SY, Joo K, et al. (2004) Prediction of protein tertiary structure using PROFESY, anovel method based on fragment assembly and conformational space annealing. <strong>Protein</strong>s56(4):704–714Lee MC, Duan Y (2004) Distinguish protein decoys by using a scoring function based on a newAMBER force field, short molecular dynamics simulations, and the generalized born solventmodel. <strong>Protein</strong>s 55(3):620–634Lee MR, Tsai J, Baker D, et al. (2001) Molecular dynamics in the endgame of protein structureprediction. J Mol Biol 313(2):417–430Levitt M, Hirshberg M, Sharon R, et al. (1995) Potential-energy function and parameters for simulationsof the molecular-dynamics of proteins and nucleic-acids in solution. Comput PhysCommun 91(1–3):215–231

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

Saved successfully!

Ooh no, something went wrong!