Bibliography

Altschul and Gish, 1996
Altschul, S. F. and Gish, W. (1996).
Local alignment statistics.
Methods Enzymol, 266:460-480.

Altschul et al., 1990
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990).
Basic local alignment search tool.
J Mol Biol, 215(3):403-410.

Andrade et al., 1998
Andrade, M. A., O'Donoghue, S. I., and Rost, B. (1998).
Adaptation of protein surfaces to subcellular location.
J Mol Biol, 276(2):517-525.

Bachmair et al., 1986
Bachmair, A., Finley, D., and Varshavsky, A. (1986).
In vivo half-life of a protein is a function of its amino-terminal residue.
Science, 234(4773):179-186.

Bateman et al., 2004
Bateman, A., Coin, L., Durbin, R., Finn, R. D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E. L., Studholme, D. J., Yeats, C., and Eddy, S. R. (2004).
The Pfam protein families database.
Nucleic Acids Res., 32(Database issue):D138-D141.

Bendtsen et al., 2004a
Bendtsen, J. D., Jensen, L. J., Blom, N., Heijne, G. V., and Brunak, S. (2004a).
Feature-based prediction of non-classical and leaderless protein secretion.
Protein Eng Des Sel, 17(4):349-356.

Bendtsen et al., 2005
Bendtsen, J. D., Kiemer, L., Fausbøll, A., and Brunak, S. (2005).
Non-classical protein secretion in bacteria.
BMC Microbiol, 5:58.

Bendtsen et al., 2004b
Bendtsen, J. D., Nielsen, H., von Heijne, G., and Brunak, S. (2004b).
Improved prediction of signal peptides: SignalP 3.0.
J Mol Biol, 340(4):783-795.

Berman et al., 2003
Berman, H., Henrick, K., and Nakamura, H. (2003).
Announcing the worldwide protein data bank.
Nat Struct Biol, 10(12):980.

Blobel, 2000
Blobel, G. (2000).
Protein targeting (Nobel lecture).
Chembiochem., 1:86-102.

Cheng et al., 2007a
Cheng, A. C., Coleman, R. G., Smyth, K. T., Cao, Q., Soulard, P., Caffrey, D. R., Salzberg, A. C., and Huang, E. S. (2007a).
Structure-based maximal affinity model predicts small-molecule druggability.
Nat Biotechnol, 25(1):71-75.

Cheng et al., 2007b
Cheng, T., Zhao, Y., Li, X., Lin, F., Xu, Y., Zhang, X., Li, Y., and Wang, R. (2007b).
Computation of octanol-water partition coefficients by guiding an additive model with knowledge.
J. Chem. Inf. Model., 47:2140-2148.

Cornette et al., 1987
Cornette, J. L., Cease, K. B., Margalit, H., Spouge, J. L., Berzofsky, J. A., and DeLisi, C. (1987).
Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins.
J Mol Biol, 195(3):659-685.

Crooks et al., 2004
Crooks, G. E., Hon, G., Chandonia, J.-M., and Brenner, S. E. (2004).
WebLogo: a sequence logo generator.
Genome Res, 14(6):1188-1190.

Dalby et al., 1992
Dalby, A., Nourse, J. G., Hounshell, W. D., Gushurst, A. K. I., Grier, D. L., Leland, B. A., and Laufer, J. (1992).
Description of several chemical structure file formats used by computer programs developed at molecular design limited.
Journal of Chemical Information and Computer Sciences, 32 (3):244-255.

Dayhoff and Schwartz, 1978
Dayhoff, M. O. and Schwartz, R. M. (1978).
Atlas of Protein Sequence and Structure, volume 3 of 5 suppl., pages 353-358.
Nat. Biomed. Res. Found., Washington D.C.

Eddy, 2004
Eddy, S. R. (2004).
Where did the BLOSUM62 alignment score matrix come from?
Nat Biotechnol, 22(8):1035-1036.

Efron, 1982
Efron, B. (1982).
The jackknife, the bootstrap and other resampling plans, volume 38.
SIAM.

Eisenberg et al., 1984
Eisenberg, D., Schwarz, E., Komaromy, M., and Wall, R. (1984).
Analysis of membrane and surface protein sequences with the hydrophobic moment plot.
J Mol Biol, 179(1):125-142.

Emini et al., 1985
Emini, E. A., Hughes, J. V., Perlow, D. S., and Boger, J. (1985).
Induction of hepatitis a virus-neutralizing antibody by a virus-specific synthetic peptide.
J Virol, 55(3):836-839.

Engelman et al., 1986
Engelman, D. M., Steitz, T. A., and Goldman, A. (1986).
Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins.
Annu Rev Biophys Biophys Chem, 15:321-353.

Felsenstein, 1985
Felsenstein, J. (1985).
Confidence limits on phylogenies: An approach using the bootstrap.
Journal of Molecular Evolution, 39:783-791.

Feng and Doolittle, 1987
Feng, D. F. and Doolittle, R. F. (1987).
Progressive sequence alignment as a prerequisite to correct phylogenetic trees.
J Mol Evol, 25(4):351-360.

Forsberg et al., 2001
Forsberg, R., Oleksiewicz, M. B., Petersen, A. M., Hein, J., Bøtner, A., and Storgaard, T. (2001).
A molecular clock dates the common ancestor of European-type porcine reproductive and respiratory syndrome virus at more than 10 years before the emergence of disease.
Virology, 289(2):174-179.

Galperin and Koonin, 1998
Galperin, M. Y. and Koonin, E. V. (1998).
Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption.
In Silico Biol, 1(1):55-67.

Gill and von Hippel, 1989
Gill, S. C. and von Hippel, P. H. (1989).
Calculation of protein extinction coefficients from amino acid sequence data.
Anal Biochem, 182(2):319-326.

Gonda et al., 1989
Gonda, D. K., Bachmair, A., Wünning, I., Tobias, J. W., Lane, W. S., and Varshavsky, A. (1989).
Universality and structure of the N-end rule.
J Biol Chem, 264(28):16700-16712.

Halgren, 1996
Halgren, T. A. (1996).
Merck molecular force field. i. basis, form, scope, parameterization, and performance of mmff94.
Journal of Computational Chemistry, 17(5-6):490-519.

Hein, 2001
Hein, J. (2001).
An algorithm for statistical alignment of sequences related by a binary tree.
In Pacific Symposium on Biocomputing, page 179.

Hein et al., 2000
Hein, J., Wiuf, C., Knudsen, B., Møller, M. B., and Wibling, G. (2000).
Statistical alignment: computational properties, homology testing and goodness-of-fit.
J Mol Biol, 302(1):265-279.

Henikoff and Henikoff, 1992
Henikoff, S. and Henikoff, J. G. (1992).
Amino acid substitution matrices from protein blocks.
Proc Natl Acad Sci U S A, 89(22):10915-10919.

Hopp and Woods, 1983
Hopp, T. P. and Woods, K. R. (1983).
A computer program for predicting protein antigenic determinants.
Mol Immunol, 20(4):483-489.

Ikai, 1980
Ikai, A. (1980).
Thermostability and aliphatic index of globular proteins.
J Biochem (Tokyo), 88(6):1895-1898.

Janin, 1979
Janin, J. (1979).
Surface and inside volumes in globular proteins.
Nature, 277(5696):491-492.

Karplus and Schulz, 1985
Karplus, P. A. and Schulz, G. E. (1985).
Prediction of chain flexibility in proteins.
Naturwissenschaften, 72:212-213.

Klee and Ellis, 2005
Klee, E. W. and Ellis, L. B. M. (2005).
Evaluating eukaryotic secreted protein prediction.
BMC Bioinformatics, 6:256.

Knudsen and Miyamoto, 2001
Knudsen, B. and Miyamoto, M. M. (2001).
A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins.
Proc Natl Acad Sci U S A, 98(25):14512-14517.

Knudsen and Miyamoto, 2003
Knudsen, B. and Miyamoto, M. M. (2003).
Sequence alignments and pair hidden markov models using evolutionary history.
Journal of Molecular Biology, 333(2):453 - 460.

Kolaskar and Tongaonkar, 1990
Kolaskar, A. S. and Tongaonkar, P. C. (1990).
A semi-empirical method for prediction of antigenic determinants on protein antigens.
FEBS Lett, 276(1-2):172-174.

Korb et al., 2009
Korb, O., Stützle, T., and Exner, T. E. (2009).
Empirical scoring functions for advanced protein-ligand docking with plants.
J Chem Inf Model, 49(1):84-96.

Kyte and Doolittle, 1982
Kyte, J. and Doolittle, R. F. (1982).
A simple method for displaying the hydropathic character of a protein.
J Mol Biol, 157(1):105-132.

Leitner and Albert, 1999
Leitner, T. and Albert, J. (1999).
The molecular clock of HIV-1 unveiled through analysis of a known transmission history.
Proc Natl Acad Sci U S A, 96(19):10752-10757.

Li et al., 2008
Li, B., Turuvekere, S., Agrawal, M., La, D., Ramani, K., and Kihara, D. (2008).
Characterization of local geometry of protein surfaces with the visibility criterion.
Proteins, 71(2):670-683.

Lipinski et al., 2001
Lipinski, C. A., Lombardo, F., Dominy, B. W., and Feeney, P. J. (2001).
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings.
Advanced Drug Delivery Reviews, 46:3-26.

Lu et al., 2008
Lu, M., Dousis, A. D., and Ma, J. (2008).
Opus-rota: A fast and accurate method for side-chain modeling.
Protein Science, 17(9):1576-1585.

Maizel and Lenk, 1981
Maizel, J. V. and Lenk, R. P. (1981).
Enhanced graphic matrix analysis of nucleic acid and protein sequences.
Proc Natl Acad Sci U S A, 78(12):7665-7669.

McGinnis and Madden, 2004
McGinnis, S. and Madden, T. L. (2004).
BLAST: at the core of a powerful and diverse set of sequence analysis tools.
Nucleic Acids Res, 32(Web Server issue):W20-W25.

Menne et al., 2000
Menne, K. M., Hermjakob, H., and Apweiler, R. (2000).
A comparison of signal sequence prediction methods using a test set of signal peptides.
Bioinformatics, 16(8):741-742.

Miao et al., 2011
Miao, Z., Cao, Y., and Jiang, T. (2011).
Rasp: rapid modeling of protein side chain conformations.
Bioinformatics, 27(22):3117-3122.

Michener and Sokal, 1957
Michener, C. and Sokal, R. (1957).
A quantitative approach to a problem in classification.
Evolution, 11:130-162.

Mukherjee and Zhang, 2009
Mukherjee, S. and Zhang, Y. (2009).
MM-align: A quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming.
Nucleic Acids Res., 37.

Nelder and Mead, 1965
Nelder and Mead (1965).
A simplex method for function minimization.
Computer Journal, 7:308-313.

Nielsen et al., 1997
Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. (1997).
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
Protein Eng, 10(1):1-6.

Purvis, 1995
Purvis, A. (1995).
A composite estimate of primate phylogeny.
Philos Trans R Soc Lond B Biol Sci, 348(1326):405-421.

Reinhardt and Hubbard, 1998
Reinhardt, A. and Hubbard, T. (1998).
Using neural networks for prediction of the subcellular location of proteins.
Nucleic Acids Res, 26(9):2230-2236.

Rose et al., 1985
Rose, G. D., Geselowitz, A. R., Lesser, G. J., Lee, R. H., and Zehfus, M. H. (1985).
Hydrophobicity of amino acid residues in globular proteins.
Science, 229(4716):834-838.

Rost, 2001
Rost, B. (2001).
Review: protein secondary structure prediction continues to rise.
J Struct Biol, 134(2-3):204-218.

Saitou and Nei, 1987
Saitou, N. and Nei, M. (1987).
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Mol Biol Evol, 4(4):406-425.

Schneider and Stephens, 1990
Schneider, T. D. and Stephens, R. M. (1990).
Sequence logos: a new way to display consensus sequences.
Nucleic Acids Res, 18(20):6097-6100.

Siepel and Haussler, 2004
Siepel, A. and Haussler, D. (2004).
Combining phylogenetic and hidden Markov models in biosequence analysis.
J Comput Biol, 11(2-3):413-428.

Smith and Waterman, 1981
Smith, T. F. and Waterman, M. S. (1981).
Identification of common molecular subsequences.
J Mol Biol, 147(1):195-197.

Tobias et al., 1991
Tobias, J. W., Shrader, T. E., Rocap, G., and Varshavsky, A. (1991).
The N-end rule in bacteria.
Science, 254(5036):1374-1377.

Vainio and Johnson, 2007
Vainio, M. J. and Johnson, M. S. (2007).
Generating conformer ensembles using a multiobjective genetic algorithm.
J Chem Inf Model, 47(6):2462-2474.

von Heijne, 1986
von Heijne, G. (1986).
A new method for predicting signal sequence cleavage sites.
Nucl. Acids Res., 14:4683-4690.

Welling et al., 1985
Welling, G. W., Weijer, W. J., van der Zee, R., and Welling-Wester, S. (1985).
Prediction of sequential antigenic regions in proteins.
FEBS Lett, 188(2):215-218.

Wootton and Federhen, 1993
Wootton, J. C. and Federhen, S. (1993).
Statistics of local complexity in amino acid sequences and sequence databases.
Computers in Chemistry, 17:149-163.

Xu and Zhang, 2010
Xu, J. and Zhang, Y. (2010).
How significant is a protein structure similarity with TM-score = 0.5?
Bioinformatics, 26(7):889-95.

Zhang and Skolnick, 2004
Zhang, Y. and Skolnick, J. (2004).
Scoring function for automated assessment of protein structure template quality.
Proteins, 57(4):702-10.

----------------------------------

#35874#>