Proteins: Structure, Function, and Bioinformatics

Getie M, Schmelzer CEH, Neubert RHH (2005) Proteins Structure, Function and Bioinformatics 61 649-657... 

Moroy G, Ostuni A, Pepe A, Tamburro AM, Alix AJP, Hery-Huynh S (2009) Proteins-Structure Function and Bioinformatics 76 461 76... 

For a reference supporting the importance of Arg358 and Phe357 for DPP-4 selectivity, see Rummy, C. and Metz, G. (2007) Homology models of dipeptidyl peptidases 8 and 9 with a focus on lop predictions near the active site. Proteins Structure, Function, and Bioinformatics, 66, 160-171. 

Kus, B., Caldon, C. E., Andorn-Broza, R., and Edwards, A. M. Functional interactions of 13 yeast SCF complexes with a set of yeast F2 enzymes in vitro. Proteins Structure, Function, and Bioinformatics 2004, 54, 455-67. 

David, G. (2005) Covell Linking tumor cell cytotoxicity to mechanism of drug action An integrated analysis of gene expression, small-molecule screening and structural databases. Proteins Structure, Function, and Bioinformatics, 59 (3), 403-433. 

Taylor, J. D., Gilbert, P J., Williams, M. A., Pitt, W. R., and Ladbury, J. E. (2007). Identification of novel fragment compounds targeted against the pY pocket of v-Src SH2 by computational and NMR screening and thermodynamic evaluation. Proteins Structure Function and Bioinformatics 67, 981-990. 

Nagano N, Noguchi T, Akiyama Y (2007) Proteins-Structure Function and Bioinformatics 66 147... 

T. A. Knotts, N. Rathore, and J. J. de Pablo (2005) Structure and stability of a model three-helix-bundle protein on tailored surfaces. Proteins-Structure Function and bioinformatics 61, pp. 385-397... 

Y. Mu, P. H. Nguyen, and G. Stock (2004) Energy landscape of a small peptide revealed by dihedral angle principal component analysis. Proteins Structure, Function, and Bioinformatics 58(1), pp. 45-52... 

He X. Mei Y. Xiang Y, et al. Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations. Proteins Structure. Function, and Bioinformatics 2005 61 423-432. 

Li, H., Robertson, A., and Jensen, J. (2005) Very fast empirical prediction and rationalization of protein pK values. Proteins Structure, Function, and Bioinformatics, 61, 704—721. 

Panigrahi, S.K. and Desiraju, G.R. (2007) Strong and weak hydrogen bonds in the protein-ligand interface. Proteins Structure, Function, and Bioinformatics, 67, 128-141. 

M.F., Olson, A.J., and Goodsell, D.S. (2002) Automated docking to multiple target structures incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins Structure, Function, and Bioinformatics, 46, 34-. ... 

Eisen, M.B., Wiley, D.C., Karplus, M., and Hubbard, R.E. (1994) HOOK a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule hinding site. Proteins Structure, Function, and Bioinformatics, 19, 199-221. 

Kolb, P., Berset, C., Huang, D and Caflisch, A. (2008) Structure-based tailoring of compound libraries for high-throughput screening discovery of novel EphB4 kinase inhibitors. Proteins Structure, Function, and Bioinformatics, 73, 11-18. 

Naor, M.M., Jensen, J.H. Proteins-Structure Function and Bioinformatics 2004,57, 799. 

Watanabe, H. C., T. Ishikura, et al. (2009). Theoretical modeling of the O-intermediate structure of bacteriorhodopsin. Proteins Structure, Function, and Bioinformatics 75(1) 53-61. 

PeUequer, J.-L., Chen, S.-w. W. (2006). Multi-template approach to modeling engineered disulfide bonds. Proteins Structure, Function, and Bioinformatics, 65(1), 192—202. http //dx. doi.org/10.1002/prot.21059. 

Anton, M., D. W. Bolen and J. Rosgen. 2008. Structural thermodynamics of protein preferential solvation Osmolyte solvation of proteins, aminoacids, and peptides. Proteins Structure, Function, and Bioinformatics. 73, 802. 

Day, R., D. Paschek, and A. E. Garcia. 2010. Microsecond simulations of the folding/unfolding thermodynamics of the Tip-cage miniprotein. Proteins Structure, Function, and Bioinformatics. 78, 1889. 

O. F. Lange and D. Baker, Proteins-Structure Function and Bioinformatics, 2012, 80, 884-895. 

B. Bardiaux, A. Bernard, W. Rieping, M. Habeck, T. E. Malliavin and M. Nilges, Proteins-Structure Function and Bioinformatics, 2009, 75, 569-585. 

T. Yamane, H. Okamura, M. Ikeguchi, Y. Nishimura and A. Kidera, Proteins-Structure Function and Bioinformatics, 2008, 71, 1970-1983. 

Lu, H. Schulten, K. (1999). Steered molecular dynamics simulations of force-induced protein domain unfolding. Proteins Structure, Function, and Bioinformatics, Vol.35, No.4, pp. 453-463... 

Porollo, A., Meller, J. (2007). Prediction-based fingerprints of protein interactions. Proteins Structure Functional and Bioinformatics, 66,... 

Hornak, V, Abel, R., Okur, A., Strockbine, B., Roit-berg. A., 8c Simmerling, C. (2006). Comparison of multiple AMBER force fields and development of improved protein backbone parameters. Proteins Structure, Function, and Bioinformatics, 65,712. 

Khafizov, K., Lattanzi,G., 8cCarloni,P. (2009). G protein inactive and active forms investigated by simulation methods. Proteins-Structure Function and Bioinformatics, 75, 919. 

D. Frishman and P. Argos, Proteins Structure, Function, and Bioinformatics, 23(4), 566-579 (1995). Knowledge-Based Protein Secondary Structure Assignment. 

Murashima, K Kosugi, A Doi, RH. Solubilization of cellulosomal cellulases by fusion with cellulose-binding domain of noncellulosomal cellulase engd from Clostridium cellulovorans. Proteins Structure, Function, and Bioinformatics, 2003, 50(4), 620 - 8. 

---