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Genomic fold assignment and rational modeling of proteins of biological interest

J M Sauder, R L Dunbrack
<span title="">2000</span> <i > <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q33b3suvffclbkvfvrsg3ljwjm" style="color: black;">Proceedings. International Conference on Intelligent Systems for Molecular Biology</a> </i> &nbsp;
The first available genome of a multicellular organism, C. elegans, was used as a test case for protein fold assignment using PSI-BLAST, followed by rational structure modeling and interpretation of experimental  ...  Similar results are demonstrated for human disease proteins with known polymorphisms.  ...  This work was funded in part by grant CA06927 from the National Institutes of Health, a grant from the American Cancer Society, and an appropriation from the Commonwealth of Pennsylvania.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10977091">pmid:10977091</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fbrrgy37mfdfjprkc2goicsihi">fatcat:fbrrgy37mfdfjprkc2goicsihi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20151027142524/http://www.aaai.org/Papers/ISMB/2000/ISMB00-031.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7d/a1/7da10c4138c73d0471b16d1282451c0f016f30d1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

Methodologies for target selection in structural genomics

Michal Linial, Golan Yona
<span title="">2000</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r3iw4i7vsvg3baci7ij2v5osfu" style="color: black;">Progress in Biophysics and Molecular Biology</a> </i> &nbsp;
As the number of complete genomes that have been sequenced keeps growing, unknown areas of the protein space are revealed and new horizons open up.  ...  We will discuss the concept of representative structures/folds, the current methodologies for identifying those proteins, and computational techniques for identifying proteins which are expected to adopt  ...  Moult and C. Sander for providing these unpublished results. This study was partially supported by the Israeli Academy of Science (Initiatives in Res. in Sc. & Technology) and the Horowitz Fund.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0079-6107(00)00011-0">doi:10.1016/s0079-6107(00)00011-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11063777">pmid:11063777</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/c3p5c6xh6jfe7j7apxdnobozwe">fatcat:c3p5c6xh6jfe7j7apxdnobozwe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20050601123507/http://www.ls.huji.ac.il:80/~michall/papers/Yona-methods-paper.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/36/22/3622115f24a88bf67680294078551267b7f6c927.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0079-6107(00)00011-0"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Structures in systems biology

Pedro Beltrao, Christina Kiel, Luis Serrano
<span title="">2007</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/uzv6ve6frfevrcjkqzfvw36bfu" style="color: black;">Current Opinion in Structural Biology</a> </i> &nbsp;
Structures of macromolecules, especially molecular machines, could provide quantitative parameters, help to elucidate functional networks or enable rational designed perturbation experiments for reverse  ...  Oil and water do not normally mix, and apparently structural biology and systems biology look like two different universes.  ...  Pedro Beltrao is supported by a grant from Fundação para a Ciência e Tecnologia through the Graduate Program in Areas of Basic and Applied Biology.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.sbi.2007.05.005">doi:10.1016/j.sbi.2007.05.005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17574836">pmid:17574836</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dayrq6t5kjfrjd55gbomzt4kza">fatcat:dayrq6t5kjfrjd55gbomzt4kza</a> </span>
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What is bioinformatics? A proposed definition and overview of the field

N M Luscombe, D Greenbaum, M Gerstein
<span title="">2001</span> <i title="Thieme (Methods of Information in Medicine)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7rg5h5xpe5fghfe7wwstoiuubm" style="color: black;">Methods of Information in Medicine</a> </i> &nbsp;
of protein structure and function, gene finding, and expression data clustering.  ...  The recent flood of data from genome sequences and functional genomics has given rise to new field, bioinformatics, which combines elements of biology and computer science.  ...  of the protein of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11552348">pmid:11552348</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mdkk5ej4ojfirplzwvqpdj3kvm">fatcat:mdkk5ej4ojfirplzwvqpdj3kvm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110331232351/http://papers.gersteinlab.org/e-print/whatis-mim/gerstein_manuscript.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/69/17/69179d08767615f3b504b20343f927c5258e6625.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

What is bioinformatics? An introduction and overview

N.M. Luscombe, D. Greenbaum, M. Gerstein
<span title="">2001</span> <i title="Georg Thieme Verlag KG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/25ybzim6mvglde3zgjvka7ehii" style="color: black;">IMIA Yearbook of Medical Informatics</a> </i> &nbsp;
of the protein of interest.  ...  Research includes characterisation of protein content and metabolic pathways between different genomes, identification of interacting proteins, assignment and prediction of gene products, and large-scale  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1055/s-0038-1638103">doi:10.1055/s-0038-1638103</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6tliu7x6eveuxnuozndgva3gyi">fatcat:6tliu7x6eveuxnuozndgva3gyi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724150339/https://www.thieme-connect.de/products/ejournals/pdf/10.1055/s-0038-1638103.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/df/3d/df3d582081c7d6110b032b9dfe6362ca8cbae797.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1055/s-0038-1638103"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

What is bioinformatics? An introduction and overview

N M Luscombe, D Greenbaum, M Gerstein
<span title="">2001</span> <i title="Georg Thieme Verlag KG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/25ybzim6mvglde3zgjvka7ehii" style="color: black;">IMIA Yearbook of Medical Informatics</a> </i> &nbsp;
of the protein of interest.  ...  Research includes characterisation of protein content and metabolic pathways between different genomes, identification of interacting proteins, assignment and prediction of gene products, and large-scale  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27701604">pmid:27701604</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rcu6325chncknf4vsy567uv7ky">fatcat:rcu6325chncknf4vsy567uv7ky</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200709024640/https://www.thieme-connect.com/products/ejournals/pdf/10.1055/s-0038-1638103.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ee/30/ee302f78b30a0950056d77d6847f0d7148d6cd32.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

Algorithmic Challenges in Structural Molecular Biology and Proteomics [chapter]

Bruce Randall Donald
<span title="2005-10-12">2005</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lirc5icuifhy7ln5rynpn4ak2e" style="color: black;">Springer Tracts in Advanced Robotics</a> </i> &nbsp;
4] , disease classification using mass spectrometry of human serum [12] , and protein redesign [13] .  ...  Concomitantly, a wealth of interesting computational problems arise in proposed methods for discovering new pharmaceuticals.  ...  One goal of the structural genomics initiative is the identification of new protein folds.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/10991541_1">doi:10.1007/10991541_1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qkbkd2pswfdyngc2zxkmrnnw6y">fatcat:qkbkd2pswfdyngc2zxkmrnnw6y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170923005922/https://users.cs.duke.edu/~brd/papers/src-papers/2004/wafr04.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/62/69/62699160363cdfbacc74cf48afdae48f68a87696.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/10991541_1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Structural proteomics: developments in structure-to-function predictions

Martin Norin, Michael Sundström
<span title="">2002</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/va62z7g5ofgoday6mzmc4uzqgm" style="color: black;">Trends in Biotechnology</a> </i> &nbsp;
The major challenge for post-genomic research is to functionally assign and validate a large number of novel target genes and their corresponding proteins.  ...  In recent reports on the sequencing and initial analysis of the human genome [1,2] the research groups computationally assigned functional categories for 40-60% of the predicted genes.  ...  Acknowledgements We are grateful to Derek Ogg at Biovitrum for valuable input during the final preparation of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0167-7799(01)01884-4">doi:10.1016/s0167-7799(01)01884-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11814598">pmid:11814598</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iidrkauqdvambgqjx2kxg5w2iq">fatcat:iidrkauqdvambgqjx2kxg5w2iq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224170714/http://pdfs.semanticscholar.org/5873/78c7187ec8a7e41c6dd4d5a27391000f3452.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/58/73/587378c7187ec8a7e41c6dd4d5a27391000f3452.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0167-7799(01)01884-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Structural and Functional Characterization of Gene Products Encoded in the Human Genome by Homology Detection

Pandit SB, Balaji S, Srinivasan N
<span title="2004-06-01">2004</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3wt2jxrnqbg5zdmkbdtjodprki" style="color: black;">IUBMB Life - A Journal of the International Union of Biochemistry and Molecular Biology</a> </i> &nbsp;
Availability of the human genome data has enabled the exploration of a huge amount of biological information encoded in it.  ...  Using the superfamily relationships between families of unknown and known structures we could increase structural information content of the human genome by about 5%.  ...  ACKNOWLEDGEMENTS This research is supported by the award of Senior Fellowship to N.S. by the Wellcome Trust, London as well as by the computational genomics initiative supported by the Department of Biotechnology  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/15216540400006105">doi:10.1080/15216540400006105</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15370880">pmid:15370880</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4savoyba7vgyvgzmpgrotrxfci">fatcat:4savoyba7vgyvgzmpgrotrxfci</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120130185650/http://nslab.mbu.iisc.ernet.in/082.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/61/f0/61f067be2c3cb09dbc0484820b05ebe8d7a2aa47.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/15216540400006105"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

NMR in structural genomics to increase structural coverage of the protein universe

Pedro Serrano, Samit K. Dutta, Andrew Proudfoot, Biswaranjan Mohanty, Lukas Susac, Bryan Martin, Michael Geralt, Lukasz Jaroszewski, Adam Godzik, Marc Elsliger, Ian A. Wilson, Kurt Wüthrich
<span title="2016-06-09">2016</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6sl6l3ojendhnjf3odmmtutouq" style="color: black;">The FEBS Journal</a> </i> &nbsp;
Furthermore, the experimental structures could be leveraged by homology modeling to further expand the structural coverage of the protein universe and increase biological insights.  ...  and could make significant contributions to biological and biomedical research.  ...  Kurt Wüthrich is the Cecil H. and Ida M. Green Professor of Structural Biology at TSRI. We thank the JCSG Crystallomics Core for providing us with clones of the presently discussed proteins.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/febs.13751">doi:10.1111/febs.13751</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27154589">pmid:27154589</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5099109/">pmcid:PMC5099109</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qof7c354erdhho3winsnufknv4">fatcat:qof7c354erdhho3winsnufknv4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191120171901/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5099109&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/10/f6/10f632343d5d8509deb6efa811961f60fda394a4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/febs.13751"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5099109" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome-based structural biology

Dmitrij Frishman, Hans-Werner Mewes
<span title="">1999</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r3iw4i7vsvg3baci7ij2v5osfu" style="color: black;">Progress in Biophysics and Molecular Biology</a> </i> &nbsp;
In this revew we consider new computational approaches and results in protein structure analysis stemming from the availability of complete genomes. #  ...  Spectacular achievements in whole genome sequencing open up new possibilities for structural research. Protein structures can now be studied in their natural genomic context.  ...  Sa nchez and Sali (1998) were able to generate allatom 3D models for 1071 S. cerevisiae gene products (17%) through a combination of fold assignment and homology modeling techniques. 236 of these proteins  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0079-6107(98)00057-1">doi:10.1016/s0079-6107(98)00057-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10446500">pmid:10446500</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e63eljdjn5hczcswaikr4xg66q">fatcat:e63eljdjn5hczcswaikr4xg66q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809070632/http://pbil.univ-lyon1.fr/members/lobry/articles/gene_1997_205_309.kim/FrishmanD1999.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fc/3c/fc3c47183895d635ad11d808e6ba2443f6c413d1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0079-6107(98)00057-1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Machine Learning in Computational Biology [chapter]

Cornelia Caragea, Vasant Honavar, Peter Boncz, Peter Boncz, Per-Åke Larson, Suzanne W. Dietrich, Gonzalo Navarro, Bhavani Thuraisingham, Yan Luo, Ouri Wolfson, Steven M. Beitzel, Eric C. Jensen (+89 others)
<span title="">2009</span> <i title="Springer US"> Encyclopedia of Database Systems </i> &nbsp;
Machine learning [6] currently offers some of the most cost-effective tools for building predictive models from biological data, e.g., for annotating new genomic sequences, for predicting macromolecular  ...  function, for identifying functionally important sites in proteins, for identifying genetic markers of diseases, and for discovering the networks of genetic interactions that orchestrate important biological  ...  Discovery and analysis of gene and protein networks: Understanding how the parts of biological systems (e.g., genes, proteins, metabolites) work together to form dynamic functional units, e.g., how genetic  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-0-387-39940-9_636">doi:10.1007/978-0-387-39940-9_636</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4gbqouocaff3vej6phko3jj6me">fatcat:4gbqouocaff3vej6phko3jj6me</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808041628/http://www.cse.unt.edu/~ccaragea/papers/encl08.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ac/40/ac40531062bf161720b17c10273caca4cba21493.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-0-387-39940-9_636"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

An overview of in silico protein function prediction

Roy D. Sleator, Paul Walsh
<span title="2010-02-03">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/krwaiukfbjhmjdogtoqtyibe4e" style="color: black;">Archives of Microbiology</a> </i> &nbsp;
As the protein databases continue to expand at an exponential rate, fed by daily uploads from multiple large scale genomic and metagenomic projects, the problem of assigning a function to each new protein  ...  has become the focus of signiWcant research interest in recent times.  ...  Acknowledgments The authors wish to acknowledge the Wnancial assistance of the Faculty of Engineering and Science, the Department of Biological Sciences and the Department of Computing at Cork Institute  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00203-010-0549-9">doi:10.1007/s00203-010-0549-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20127480">pmid:20127480</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/steidmwhqbhphktktb36xc4xga">fatcat:steidmwhqbhphktktb36xc4xga</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170706020023/http://curso-proteinas.cidbio.org/Functionprediction.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/13/bc/13bc39a5e7eade09e1f5f1487ef346578ccdab07.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00203-010-0549-9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

PSI-2: Structural Genomics to Cover Protein Domain Family Space

Benoît H. Dessailly, Rajesh Nair, Lukasz Jaroszewski, J. Eduardo Fajardo, Andrei Kouranov, David Lee, Andras Fiser, Adam Godzik, Burkhard Rost, Christine Orengo
<span title="">2009</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/y4oayrlrkfebxgzkm3rrzcps2m" style="color: black;">Structure</a> </i> &nbsp;
One major objective of structural genomics efforts, including the NIH-funded Protein Structure Initiative (PSI), has been to increase the structural coverage of protein sequence space.  ...  On the basis of several metrics, we then discuss to what extent PSI-2, during its first three years, has increased the structural coverage of genomes, and contributed structural and functional novelty.  ...  Acknowledgments This work was supported by a grant from the Protein Structure Initiative (PSI) of the National Institute for General Medicine at the National Institutes of Health.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.str.2009.03.015">doi:10.1016/j.str.2009.03.015</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19523904">pmid:19523904</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2920419/">pmcid:PMC2920419</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d3brqpvvqrcmhflreab6f4ohay">fatcat:d3brqpvvqrcmhflreab6f4ohay</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191111004802/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2920419&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1c/ec/1cec608cdd024744d25550c88a5f0b051057bb7d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.str.2009.03.015"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2920419" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Proteins with Class α/β Fold Have High-level Participation in Fusion Events

Sujun Hua, Tao Guo, Julian Gough, Zhirong Sun
<span title="">2002</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nk6zopmzsjfizb6z5kztdu477y" style="color: black;">Journal of Molecular Biology</a> </i> &nbsp;
An exhaustive survey of fusion events within 30 completely sequenced genomes and subsequent structure annotations to the component proteins at a SCOP superfamily level with hidden Markov models was carried  ...  The results revealed that proteins with the class a/b fold are frequently involved in fusion events, around 86% of the total 676 assigned single-domain fusion pairs including at least one component protein  ...  This work was funded by the National Natural Science Grant in China (no. 39980007) and the National Key Foundational Research Grant in China (985, 863).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0022-2836(02)00467-9">doi:10.1016/s0022-2836(02)00467-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12095249">pmid:12095249</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vjr5sn3agzhdrg6yv2onulsvda">fatcat:vjr5sn3agzhdrg6yv2onulsvda</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190305043051/http://pdfs.semanticscholar.org/e5fc/c776d4911ae44a06b69dffbb725fda4937f2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e5/fc/e5fcc776d4911ae44a06b69dffbb725fda4937f2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0022-2836(02)00467-9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>
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