@comment{{This file has been generated by bib2bib 1.97}}
@comment{{Command line: bib2bib ../bibli.bib -c 'subject:"casp" or keywords:"casp"' -ob tmp.bib}}
@article{Altschul1997Gapped,
author = {S.F. Altschul and T.L. Madden and A.A. Schaffer and J. Zhang and
Z. Zhang and W. Miller and D.J. Lipman},
title = {Gapped {BLAST} and {PSI}-{BLAST}: {A} new generation of protein database
search programs},
journal = {Nucleic {A}cids {R}esearch},
year = {1997},
volume = {25},
pages = {3389--3402},
pdf = {../local/alts97.pdf},
file = {alts97.pdf:local/alts97.pdf:PDF},
subject = {biocasp},
url = {http://nar.oupjournals.org/cgi/reprint/25/17/3389.pdf}
}
@article{Baldi1999Exploiting,
author = {Baldi, P. and Brunak, S. and Frasconi, P. and Soda, G. and Pollastri,
G.},
title = {Exploiting the past and the future in protein secondary structure
prediction},
journal = {Bioinformatics},
year = {1999},
volume = {15},
pages = {937--946},
pdf = {../local/bald99.pdf},
file = {bald99.pdf:local/bald99.pdf:PDF},
subject = {biocasp},
url = {http://bioinformatics.oupjournals.org/cgi/reprint/15/11/937.pdf}
}
@article{Cuff1999Evaluation,
author = {Cuff, J. A. and Barton, G. J.},
title = {Evaluation and improvement of multiple sequence methods for protein
secondary structure prediction},
journal = {Protein. {S}truct. {F}unct. {G}enet.},
year = {1999},
volume = {34},
pages = {508-519},
pdf = {../local/cuff99.pdf},
file = {cuff99.pdf:local/cuff99.pdf:PDF},
subject = {biocasp},
url = {http://www3.interscience.wiley.com/cgi-bin/fulltext/65000270/FILE?TPL=ft_start}
}
@article{Debouck1999DNA,
author = {C. Debouck and P. N. Goodfellow},
title = {{DNA} microarrays in drug discovery and development.},
journal = {Nat. Genet.},
year = {1999},
volume = {21},
pages = {48--50},
number = {1 Suppl},
month = {Jan},
abstract = {DNA microarrays can be used to measure the expression patterns of
thousands of genes in parallel, generating clues to gene function
that can help to identify appropriate targets for therapeutic intervention.
They can also be used to monitor changes in gene expression in response
to drug treatments. Here, we discuss the different ways in which
microarray analysis is likely to affect drug discovery.},
doi = {10.1038/4475},
keywords = {Agricultural, Alleles, Alternaria, Amino Acid, Amino Acid Chloromethyl
Ketones, Amino Acid Sequence, Animal, Animals, Apoptosis, Asthma,
Bacteria, Base Sequence, Binding Sites, Biotechnology, Blotting,
Bone Density, Bone Matrix, Bone and Bones, CCR5, Camptothecin, Caspases,
Cathepsins, Cell Surface, Central America, Chloroplast, Chondrocytes,
Chromosome Mapping, Chromosomes, Cloning, Cluster Analysis, Collagen,
Comparative Study, Coumarins, Crops, Crystallography, DNA, DNA Primers,
Dipeptides, Disease, Disease Models, Drug Design, Drug Evaluation,
Drug Industry, Enzyme Activation, Enzyme Inhibitors, Escherichia
coli, Evolution, Exons, Expressed Sequence Tags, Female, Fetus, Fluorescent
Dyes, Food Microbiology, Founder Effect, GTP-Binding Proteins, Gene
Expression, Gene Frequency, Gene Library, Genes, Genetic, Genetic
Predisposition to Disease, Genome, Geography, Growth Plate, Haplotypes,
Hordeum, Human, Humans, Inclusion Bodies, Injections, Intraperitoneal,
Introns, Isatin, Knockout, Male, Membrane Proteins, Messenger, Mice,
Models, Molecular, Molecular Sequence Data, Molecular Structure,
Mutation, Mycotoxins, Neutrophils, Non-U.S. Gov't, Northern, Oligonucleotide
Array Sequence Analysis, Osteoarthritis, Osteochondrodysplasias,
Osteoclasts, Osteopetrosis, Pair 15, Phaseolus, Polymorphism, Preclinical,
Pregnancy, Promoter Regions (Genetics), Protein Precursors, Proteomics,
RNA, Receptors, Recombinant Fusion Proteins, Recombinant Proteins,
Research Support, Restriction Fragment Length, Ribosomal Proteins,
Sequence Alignment, Sequence Analysis, Sequence Homology, South America,
Species Specificity, Splenomegaly, Sulfonamides, Synteny, Tissue
Distribution, Transcription, Trichothecenes, X-Ray, 9915501},
owner = {piedro},
pmid = {9915501},
timestamp = {2006.08.11},
url = {http://dx.doi.org/10.1038/4475}
}
@inproceedings{Grundy1998Family-based,
author = {Grundy, W. N.},
title = {Family-based {H}omology {D}etection via {P}airwise {S}equence {C}omparison},
booktitle = {Proceedings of the {S}econd {A}nnual {I}nternational {C}onference
on {C}omputational {M}olecular {B}iology, {M}arch 22-25},
year = {1998},
pages = {94--100},
pdf = {../local/grun98.pdf},
file = {grun98.pdf:local/grun98.pdf:PDF},
subject = {biocasp},
url = {http://www.cs.columbia.edu/~bgrundy/papers/compare.html}
}
@article{Jaakkola2000Discriminative,
author = {Jaakkola, T. and Diekhans, M. and Haussler, D.},
title = {A {D}iscriminative {F}ramework for {D}etecting {R}emote {P}rotein
{H}omologies},
journal = {J. {C}omput. {B}iol.},
year = {2000},
volume = {7},
pages = {95--114},
number = {1,2},
pdf = {../local/jaak00.pdf},
file = {jaak00.pdf:local/jaak00.pdf:PDF},
keywords = {biosvm},
subject = {biokernelcasp},
url = {http://www.cse.ucsc.edu/research/compbio/discriminative/Jaakola2-1998.ps}
}
@article{Karplus1998Hidden,
author = {Karplus, K. and Barrett, C. and Hughey, R.},
title = {Hidden {M}arkov {M}odels for {D}etecting {R}emote {P}rotein {H}omologies},
journal = {Bioinformatics},
year = {1998},
volume = {14},
pages = {846--856},
number = {10},
pdf = {../local/karp98.pdf},
file = {karp98.pdf:local/karp98.pdf:PDF},
subject = {biocasp},
url = {http://www.cse.ucsc.edu/research/compbio/papers/w9824.ps}
}
@inproceedings{Liao2002Combining,
author = {Liao, L. and Noble, W. S.},
title = {Combining pairwise sequence similarity and support vector machines
for remote protein homology detection},
booktitle = {Proceedings of the {S}ixth {I}nternational {C}onference on {C}omputational
{M}olecular {B}iology},
year = {2002},
pdf = {../local/liao02.pdf},
file = {liao02.pdf:local/liao02.pdf:PDF},
keywords = {biosvm},
subject = {biokernelcasp},
url = {http://www.cs.columbia.edu/~bgrundy/papers/fps-svm.html}
}
@article{Zhang2008Progress,
author = {Zhang, Yang},
title = {Progress and challenges in protein structure prediction},
journal = {Curr. Opin. Struct. Biol.},
year = {2008},
volume = {18},
pages = {342--348},
number = {3},
month = {June},
abstract = {Depending on whether similar structures are found in the PDB library,
the protein structure prediction can be categorized into template-based
modeling and free modeling. Although threading is an efficient tool
to detect the structural analogs, the advancements in methodology
development have come to a steady state. Encouraging progress is
observed in structure refinement which aims at drawing template structures
closer to the native; this has been mainly driven by the use of multiple
structure templates and the development of hybrid knowledge-based
and physics-based force fields. For free modeling, exciting examples
have been witnessed in folding small proteins to atomic resolutions.
However, predicting structures for proteins larger than 150 residues
still remains a challenge, with bottlenecks from both force field
and conformational search.},
booktitle = {Nucleic acids / Sequences and topology},
doi = {10.1016/j.sbi.2008.02.004},
keywords = {casp8, modeling, zhang},
url = {http://dx.doi.org/10.1016/j.sbi.2008.02.004}
}
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omput. Biol.;J. Biol. Chem.;J. Biomed. Inform.;J. Cell. Biochem.;J. Ch
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st.;J. Mach. Learn. Res.;J. Med. Chem.;J. Mol. BIol.;J. R. Stat. Soc.
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el.;Protein Sci.;Protein. Struct. Funct. Genet.;Random Struct. Algorit
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