\begin{thebibliography}{10}

\bibitem{UCSC-CASP2-proteins}
Kevin Karplus, Kimmen {Sj\"olander}, Christian Barrett, Melissa Cline, David
  Haussler, Richard Hughey, Liisa Holm, and Chris Sander.
\newblock Predicting protein structure using hidden {Markov} models.
\newblock {\em Proteins: Structure, Function, and Genetics}, Suppl. 1:134--139,
  1997.

\bibitem{UCSC-CASP3-proteins}
Kevin Karplus, Christian Barrett, Melissa Cline, Mark Diekhans, Leslie Grate,
  and Richard Hughey.
\newblock Predicting protein structure using only sequence information.
\newblock {\em Proteins: Structure, Function, and Genetics}, Supplement
  3(1):121--125, 1999.

\bibitem{SAMT2K-CASP4-proteins}
Kevin Karplus, Rachel Karchin, Christian Barrett, Spencer Tu, Melissa Cline,
  Mark Diekhans, Leslie Grate, Jonathan Casper, and Richard Hughey.
\newblock What is the value added by human intervention in protein structure
  prediction?
\newblock {\em Proteins: Structure, Function, and Genetics}, 45(S5):86--91,
  2001.

\bibitem{SAMT98}
Kevin Karplus, Christian Barrett, and Richard Hughey.
\newblock Hidden {Markov} models for detecting remote protein homologies.
\newblock {\em Bioinformatics}, 14(10):846--856, 1998.

\bibitem{EVA-bioinf01}
V.A. Eyrich, M.A. Marti-Renom, D.~Przybylski, M.S. Madhusudhan, A.~Fiser,
  F.~Pazos, A.~Valencia, A.~Sali, and B.~Rost.
\newblock {EVA}: continuous automatic evaluation of protein structure
  prediction servers.
\newblock {\em Bioinformatics}, 17(12):1242--1243, December 2001.

\bibitem{SAMT02-CASP5}
Kevin Karplus, Rachel Karchin, Jenny Draper, Jonathan Casper, Yael
  Mandel-Gutfreund, Mark Diekhans, and Richard Hughey.
\newblock Combining local-structure, fold-recognition, and new-fold methods for
  protein structure prediction.
\newblock {\em Proteins: Structure, Function, and Genetics}, 53(S6,
  pages=491-496), 15October 2003.

\bibitem{nr}
NR (All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Database)
  Distributed on the Internet via anonymous FTP from {\tt
  ftp://ftp.ncbi.nlm.nih.gov/blast/db}.
\newblock Information on NR is available at {\tt
  http://www.ncbi.nlm.nih.gov/\discretionary{}{}{}BLAST/\discretionary{}{}{}bl%
ast\_databases.html}.

\bibitem{BLAST}
S.~Altschul, W.~Gish, W.~Miller, E.~Myers, and D.~Lipman.
\newblock Basic local alignment search tool.
\newblock {\em Journal of Molecular Biology}, 215:403--410, 1990.

\bibitem{psiblast97}
S.~Altschul, T.~Madden, A.~Schaffer, J.~Zhang, Z.~Zhang, W.~Miller, and
  D.~Lipman.
\newblock Gapped {BLAST} and {PSI-BLAST}: A new generation of protein database
  search programs.
\newblock {\em Nucleic Acids Research}, 25:3899--3402, 1997.

\bibitem{improved-psiblast-2001}
Alejandro~A. Sch\"affer, L.~Aravind, Thomas~L. Madden, Sergei Shavirin, John~L.
  Spouge, Yuri~I. Wolf, Eugene Koonin, and Stephen~F. Altschul.
\newblock Improving the accuracy of {PSI-BLAST} protein database searches with
  composition-based statistics and other refinements.
\newblock {\em Nucleic Acids Research}, 29(14):2994--3005, 2001.

\bibitem{karchin03-backbone-geometries}
Rachel Karchin, Melissa Cline, Yael Mandel-Gutfreund, and Kevin Karplus.
\newblock Hidden {Markov} models that use predicted local structure for fold
  recognition: alphabets of backbone geometry.
\newblock {\em Proteins: Structure, Function, and Genetics}, 51(4):504--514,
  June 2003.

\bibitem{karchin-burial-alphabets}
Rachel Karchin, Melissa Cline, and Kevin Karplus.
\newblock Evaluation of local structure alphabets based on residue burial.
\newblock {\em Proteins: Structure, Function, and Genetics}, 55(3):508--518, 5
  March 2004.
\newblock Online:
  http://www3.interscience.wiley.com/cgi-bin/abstract/107632554/ABSTRACT.

\bibitem{mini-thread-CASP3}
Kim~T. Simons, Rich Bonneau, Ingo Ruczinski, and David Baker.
\newblock Ab initio protein structure prediction of {CASP III} targets using
  {ROSETTA}.
\newblock {\em Proteins: Structure, Function, and Genetics}, Supplement
  3(1):171--176, 1999.

\bibitem{SCWRL}
Michael Bower, Fred Cohen, and Roland Dunbrack.
\newblock Prediction of protein side-chain rotamers from a backbone-dependent
  rotamer library: A new homology modeling tool.
\newblock {\em Journal of Molecular Biology}, 267:1268--1282, 1997.

\bibitem{SCWRL-3.0}
Adrian~A. Canutescu, Andrew~A. Shelenkov, and Roland~L. Dunbrack~Jr.
\newblock A graph-theory algorithm for rapid protein side-chain prediction.
\newblock {\em Protein Science}, 12:2001--2014, 2003.

\bibitem{hydrophobicity-cid-pe92}
Hilda Cid, Marta Bunster, Mauricio Canales, and F.~Gazitua.
\newblock Hydrophobicity and structural classes in proteins.
\newblock {\em Protein Engineering}, 5:373--375, 1992.

\end{thebibliography}
