Download "An Introduction to Modeling Structure from Sequence". In: Current

Transcript
Koh, I.-Y.Y., Eyrich, V.A., Marti-Renom,
M.A., Przybylski, D., Madhusudhan, M.S.,
Narayanan, E., Grana, O., Pazos, F., Valencia,
A., Sali, A., and Rost, B. 2003. EVA: Evaluation
of protein structure prediction servers. Nucl.
Acids Res. 31:3311-3315.
Krogh, A., Brown, M., Mian, I.S., Sjolander, K., and
Haussler, D. 1994. Hidden Markov models in
computational biology. Applications to protein
modeling. J. Mol. Biol. 235:1501-1531.
Laskowski, R.A., MacArthur, M.W., Moss, D.S.,
and Thornton, J.M. 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26:283-291.
Laskowski, R.A., Rullmannn, J.A., MacArthur,
M.W., Kaptein, R., and Thornton, J.M. 1996.
AQUA and PROCHECK-NMR: Programs for
checking the quality of protein structures
solved by NMR. J. Biomol. NMR 8:477486.
Laskowski, R.A., MacArthur, M.W., and Thornton,
J.M. 1998. Validation of protein models derived from experiment. Curr. Opin. Struct. Biol.
8:631-639.
Lessel, U. and Schomburg, D. 1994. Similarities
between protein 3-D structures. Protein Eng.
7:1175-1187.
Levitt, M. 1992. Accurate modeling of protein
conformation by automatic segment matching.
J. Mol. Biol. 226:507-533.
Li, R., Chen, X., Gong, B., Selzer, P.M., Li, Z.,
Davidson, E., Kurzban, G., Miller, R.E., Nuzum,
E.O., McKerrow, J.H., Fletterick, R.J., Gillmor,
S.A., Craik, C.S., Kuntz, I.D., Cohen, F.E.,
and Kenyon, G.L. 1996. Structure-based design
of parasitic protease inhibitors. Bioorg. Med.
Chem. 4:1421-1427.
Mallick, P., Weiss, R., and Eisenberg, D. 2002. The
directional atomic solvation energy: An atombased potential for the assignment of protein
sequences to known folds. Proc. Natl. Acad. Sci.
U.S.A. 99:16041-16046.
Marti-Renom, M.A., Stuart, A.C., Fiser, A.,
Sanchez, R., Melo, F., and Sali, A. 2000. Comparative protein structure modeling of genes and
genomes. Annu. Rev. Biophys. Biomol. Struct.
29:291-325.
Marti-Renom, M.A., Ilyin, V.A., and Sali, A. 2001.
DBAli: A database of protein structure alignments. Bioinformatics 17:746-747.
Marti-Renom, M.A., Madhusudhan, M.S., Fiser,
A., Rost, B., and Sali, A. 2002. Reliability of
assessment of protein structure prediction methods. Structure (Camb) 10:435-440.
Marti-Renom, M.A., Madhusudhan, M.S., and Sali,
A. 2004. Alignment of protein sequences by
their profiles. Protein Sci. 13:1071-1087.
Matsumoto, R., Sali, A., Ghildyal, N., Karplus,
M., and Stevens, R.L. 1995. Packaging of proteases and proteoglycans in the granules of mast
cells and other hematopoietic cells. A cluster of
histidines on mouse mast cell protease 7 regulates its binding to heparin serglycin proteoglycans. J. Biol. Chem. 270:19524-19531.
McGuffin, L.J. and Jones, D.T. 2003. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19:874881.
McGuffin, L.J., Bryson, K., and Jones, D.T.
2000. The PSIPRED protein structure prediction server. Bioinformatics 16:404-405.
Melo, F. and Feytmans, E. 1998. Assessing protein
structures with a non-local atomic interaction
energy. J. Mol. Biol. 277:1141-1152.
Lin, J., Qian, J., Greenbaum, D., Bertone, P., Das,
R., Echols, N., Senes, A., Stenger, B., and
Gerstein, M. 2002. GeneCensus: Genome comparisons in terms of metabolic pathway activity and protein family sharing. Nucl. Acids Res.
30:4574-4582.
Melo, F., Sanchez, R., and Sali, A. 2002. Statistical potentials for fold assessment. Protein Sci.
11:430-448.
Lindahl, E. and Elofsson, A. 2000. Identification of
related proteins on family, superfamily and fold
level. J. Mol. Biol. 295:613-625.
Mirkovic, N., Marti-Renom, M.A., Sali, A., and
Monteiro, A.N.A. 2004. Structure-based assessment of missence mutations in human BRCA1:
Implications for breast and ovarian cancer predisposition. Cancer Res. 64:3790-3797.
Luthy, R., Bowie, J.U., and Eisenberg, D. 1992.
Assessment of protein models with threedimensional profiles. Nature 356:83-85.
MacKerell, A.D. Jr., Bashford, D., Bellott, M.,
Dunbrack, R.L. Jr., Evanseck, J.D., Field, M.J.,
Fischer, S., Gao, J., Guo, H., Ha, S., JosephMcCarthy, D., Kuchnir, L., Kuczera, K., Lau,
F.T.K., Mattos, C., Michnick, S., Ngo, T.,
Nguyen, D.T., Prodhom, B., Reiher, W.E. III,
Roux, B., Schlenkrich, M., Smith, J.C., Stote, R.,
Straub, J., Watanabe, M., Wiórkiewicz-Kuczera,
J., Yin, D., and Karplus, M. 1998. All-atom empirical potential for molecular modleing and dynamics studies of proteins. J. Phys. Chem. B
102:3586-3616.
Madhusudhan, M.S., Marti-Renom, M.A.,
Sanchez, R., and Sali, A. 2006. Variable
gap penalty for protein sequence-structure
alignment. Protein Eng. Des. Sel. 19:129-133.
Current Protocols in Bioinformatics
Mezei, M. 1998. Chameleon sequences in the PDB.
Protein Eng. 11:411-414.
Misura, K.M. and Baker, D. 2005. Progress and
challenges in high-resolution refinement of protein structure models. Proteins 59:15-29.
Misura, K.M., Chivian, D., Rohl, C.A., Kim, D.E.,
and Baker, D. 2006. Physically realistic homology models built with ROSETTA can be more
accurate than their templates. Proc. Natl. Acad.
Sci. U.S.A. 103:5361-5366.
Miwa, J.M., Ibanez-Tallon, I., Crabtree, G.W.,
Sanchez, R., Sali, A., Role, L.W., and Heintz,
N. 1999. lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the
mammalian CNS. Neuron 23:105-114.
Modi, S., Paine, M.J., Sutcliffe, M.J., Lian, L.Y.,
Primrose, W.U., Wolf, C.R., and Roberts, G.C.
1996. A model for human cytochrome P450 2D6
based on homology modeling and NMR studies
Modeling
Structure from
Sequence
5.6.27
Supplement 15