Bibliografía

Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997).

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic Acids Res., 25(17):3389-3402.

Bower, M. J., Cohen, F. E. & Dunbrack, R. L., J. (1997).

Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.
J.Mol.Biol., 267(5):1268-1282.

Brown, N., Leroy, C. & Sander, C. (1998).

MView: A Web compatible database search or multiple alignment viewer.
Bioinformatics, 14(4):380-381.

Chothia, C. & Lesk, A. M. (1986).

The relation between the divergence of sequence and structure in proteins.
EMBO J., 5(4):823-826.

Contreras-Moreira, B., Ezkurdia, I., Tress, M. & Valencia, A. (2005).

Empirical limits for template-based protein structure prediction: the CASP5 example.
FEBS Lett., 579(5):1203-1207.

Eddy, S. R. (2004).

What is a hidden Markov model?
Nat Biotechnol., 10(22):1315-1316.

Fiser, A. & Sali, A. (2003).

Modeller: Generation and Refinement of Homology-Based Protein Structure Models.
Methods in Enzymology, 374:461-491.

Gribskov, M., McLachlan, A. D. & Eisenberg, D. (1987).

Profile analysis: detection of distantly related proteins.
PNAS, 84(13):4355-4358.

Gusfield, D. (1997).

Algorithms on strings, trees and sequences: computer science and computationsl biology.
Cambridge University Press.

Jones, D. T. (1999).

Protein secondary structure prediction based on position-specific scoring matrices.
J.Mol.Biol., 292(2):195-202.

Kanhere, A. & Bansal, M. (2005).

A novel method for prokaryotic promoter prediction based on DNA stability.
BMC Bioinformatics, 6(1):1.

Kim, D., Chivian, D. & Baker, D. (2004).

Protein structure prediction and analysis using the Robetta server.
Nucl.Acids Res., 33 Suppl.(2):W526-531.

Michael Gromiha, M., Siebers, J., Selvaraj, S., Kono, H. & Sarai, A. ( 2004).

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.
J.Mol.Biol., 337(2):285-294.

Needleman, S. B. & Wunsch, C. D. (1970).

A general method applicable to the search for similarities in the amino acid sequence of two proteins.
J.Mol.Biol., 48:443-453.

Ortiz, A. R., Strauss, C. E. M. & Olmea, O. (2002).

MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison.
Protein Sci, 11(11):2606-2621.
Evaluation Studies.

Reina, J., Lacroix, E., Hobson, S. D., Fernandez-Ballester, G., Rybin, V., Schwab, M. S., Serrano, L. & Gonzalez, C. (2002).

Computer-aided design of a PDZ domain to recognize new target sequences.
Nat.Struct.Biol., 9(8):621-627.

Rose, T., Henikoff, J. & Henikoff, S. (2003).

CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design.
Nucleic Acids Res., 31(13):3763-3766.

Sali, A. & Blundell, T. L. (1993).

Comparative protein modelling by satisfaction of spatial restraints.
J.Mol.Biol., 234(3):779-815.

Smith, T. & Waterman, M. (1981).

Identification of Common Molecular Subsequences.
J.Mol.Biol., 147:195-197.

Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994).

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Nucleic Acids Res., 22(22):4673-4680.

Washietl, S., Hofacker, I. & Stadler, P. F. (2005).

Fast and reliable prediction of noncoding RNAs.
PNAS, 102(7):2454-2459.

Wootton, J. C. & Federhen, S. (1996).

Analysis of compositionally biased regions in sequence databases.
Methods Enzymol., 266:554-571.

Zhang, Y. & Skolnick, J. (2005).

The protein structure prediction problem could be solved using the current PDB library.
PNAS, 102:1029.