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Active site properties of monomeric triosephosphate isomerase (monoTIM) as deduced from mutational and structural studies

Wolfgang Schliebs, Narmada Thanki, Ramon Eritja, Rik Wierenga
<span title="2008-12-31">2008</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bubxfqklvdwthsc43yvjbtjae" style="color: black;">Protein Science</a> </i> &nbsp;
MonoTIM is a stable monomeric variant of the dimeric trypanosomal enzyme triose phosphate isomerase (TIM) with less, but significant, catalytic activity. It is known that in TIM, three residues, Lys 13 (loop l), His 95 (loop 4), and Glu 167 (loop 6) are the crucial catalytic residues. In the wild-type TIM dimer, loop 1 and loop 4 are very rigid because of tight interactions with residues of the other subunit. Previous structural studies indicate that Lys 13 and His 95 have much increased
more &raquo; ... ational flexibility in monoTIM. Using site-directed mutagenesis, it is shown here that Lys 13 and His 95 are nevertheless essential for optimal catalysis by monoTIM: monoTIM-K13A is completely inactive, although it can still bind substrate analogues, and monoTI"H95A is 50 times less active. The best inhibitors of wild-type TIM are phosphoglycolohydroxamate (PGH) and 2-phosphoglycolate (2PG), with K, values of 8 pM and 26 pM, respectively. The affinity of the monoTIM active site for PGH has been reduced approximately 60-fold, whereas for 2PG, only a twofold weakening of affinity is observed. The mode of binding, as determined by protein crystallographic analysis of these substrate analogues, shows that, in particular, 2PG interacts with Lys 13 and His 95 in a way similar but not identical to that observed for the wild-type enzyme. This crystallographic analysis also shows that Glu 167 has the same interactions with the substrate analogues as in the wild type. The data presented suggest that, despite the absence of the second subunit, monoTIM catalyzes the interconversion of ~-glyceraldehyde-3-phosphate and dihydroxyacetone phosphate via the same mechanism as in the wild type.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pro.5560050206">doi:10.1002/pro.5560050206</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/8745400">pmid:8745400</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2143345/">pmcid:PMC2143345</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ofhg7ugjabfmbjtpfcw62fn2ui">fatcat:ofhg7ugjabfmbjtpfcw62fn2ui</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200501222229/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2143345&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/d3/f0/d3f0d0d5de3cc219e9f259d5d2e511080dbefd29.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pro.5560050206"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143345" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Molecular classification of cancer: unsupervised self-organizing map analysis of gene expression microarray data

David G Covell, Anders Wallqvist, Alfred A Rabow, Narmada Thanki
<span title="">2003</span> <i title="American Association for Cancer Research"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fq3iu4cc7vf7nigavvtibl5d4e" style="color: black;">Molecular Cancer Therapeutics</a> </i> &nbsp;
An unsupervised self-organizing map-based clustering strategy has been developed to classify tissue samples from an oligonucleotide microarray patient database. Our method is based on the likelihood that a test data vector may have a gene expression fingerprint that is shared by more than one tumor class and as such can identify datasets that cannot be unequivocally assigned to a single tumor class. Our self-organizing map analysis completely separated the tumor from the normal expression
more &raquo; ... ts. Within the 14 different tumor types, classification accuracies on the order of approximately 80% correct were achieved. Nearly perfect classifications were found for leukemia, central nervous system, melanoma, uterine, and lymphoma tumor types, with very poor classifications found for colorectal, ovarian, breast, and lung tumors. Classification results were further analyzed to identify sets of differentially expressed genes between tumor and normal gene expressions and among each tumor class. Within the total pool of 1139 genes most differentially expressed in this dataset, subsets were found that could be vetted according to previously published literature sources to be specific tumor markers. Attempts to classify gene expression datasets from other sources found a wide range of classification accuracies. Discussions about the utility of this method and the quality of data needed for accurate tumor classifications are provided.
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12657727">pmid:12657727</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7s7yq76eyfgt5bs2lcdvprlpp4">fatcat:7s7yq76eyfgt5bs2lcdvprlpp4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170815072921/http://mct.aacrjournals.org/content/molcanther/2/3/317.full.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/87/da/87da557855a5df0b970a3a0f303bb8228d8ac187.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

Three new crystal structures of point mutation variants of mono TIM: conformational flexibility of loop-1, loop-4 and loop-8

Torben V Borchert, KV Radha Kishan, Johan Ph Zeelen, Wolfgang Schliebs, Narmada Thanki, Ruben Abagyan, Rainer Jaenicke, Rik K Wierenga
<span title="">1995</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/y4oayrlrkfebxgzkm3rrzcps2m" style="color: black;">Structure</a> </i> &nbsp;
Wild-type triosephosphate isomerase (TIM) is a very stable dimeric enzyme. This dimer can be converted into a stable monomeric protein (monoTIM) by replacing the 15-residue interface loop (loop-3) by a shorter, 8-residue, loop. The crystal structure of mono-TIM shows that two active-site loops (loop-1 and loop-4), which are at the dimer interface in wild-type TIM, have acquired rather different structural properties. Nevertheless, monoTIM has residual catalytic activity. Results: Three new
more &raquo; ... tures of variants of monoTIM are presented, a double-point mutant crystallized in the presence and absence of bound inhibitor, and a singlepoint mutant in the presence of a different inhibitor. These new structures show large structural variability for the active-site loops, loop-1, loop-4 and loop-8. In the structures with inhibitor bound, the catalytic lysine (Lysl3 in loop-1) and the catalytic histidine (His95 in loop-4) adopt conformations similar to those observed in wild-type TIM, but very different from the monoTIM structure. Conclusions: The residual catalytic activity of mono-TIM can now be rationalized. In the presence of substrate analogues the active-site loops, loop-1, loop-4 and loop-8, as well as the catalytic residues, adopt conformations similar to those seen in the wild-type protein. These loops lack conformational flexibility in wild-type TIM. The data suggest that the rigidity of these loops in wildtype TIM, resulting from subunit-subunit contacts at the dimer interface, is important for optimal catalysis.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0969-2126(01)00202-7">doi:10.1016/s0969-2126(01)00202-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/8591044">pmid:8591044</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uhfgntpw7zalfj2o5jfsfnyscu">fatcat:uhfgntpw7zalfj2o5jfsfnyscu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171002025948/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/af2/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDk2OTIxMjYwMTAwMjAyNw%3D%3D.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/cf/57/cf578080334ad5827de16ba5afb5d8564c53469c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0969-2126(01)00202-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

The Protein Data Bank

Helen M. Berman, Tammy Battistuz, T. N. Bhat, Wolfgang F. Bluhm, Philip E. Bourne, Kyle Burkhardt, Zukang Feng, Gary L. Gilliland, Lisa Iype, Shri Jain, Phoebe Fagan, Jessica Marvin (+7 others)
<span title="2002-05-29">2002</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6inoqqfovnhtledhw3uuo322xa" style="color: black;">Acta Crystallographica Section D: Biological Crystallography</a> </i> &nbsp;
The Protein Data Bank [PDB; Berman, Westbrooket al.(2000),Nucleic Acids Res.28, 235–242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules. Many secondary sources of information are derived from PDB data. It is the starting point for studies in structural bioinformatics. This article describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information and plans for the future development
more &raquo; ... of the resource. The reader should come away with an understanding of the scope of the PDB and what is provided by the resource.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444902003451">doi:10.1107/s0907444902003451</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12037327">pmid:12037327</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/satbdpl4a5c2jk7uo42ovv2dgm">fatcat:satbdpl4a5c2jk7uo42ovv2dgm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20040714021133/http://www.cstl.nist.gov:80/div831/carb/gilliland_group/abstracts/acd58-899.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/f7/9f/f79faf3f6683805c065348d16fa8335bdd460964.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444902003451"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Comparison of calcium-dependent conformational changes in the N-terminal SH2 domains of p85 and gap defines distinct properties for SH2 domains

Daruka Mahadevan, Narmada Thanki, Peter McPhie, John F. Beeler, Jin Chen Yu, Alexander Wlodawer, Mohammad A. Heidaran
<span title="">1994</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4qyryvw5mvde5nt6xjruewxve4" style="color: black;">Biochemistry</a> </i> &nbsp;
Src-homology region 2 (SH2) domains are stretches of about 100 amino acids which are found to be structurally conserved in a number of signaling molecules. These regions have been shown to bind with high affinity to phosphotyrosine residues within activated receptor tyrosine kinases. Here we report the bacterial expression and purification of individual N-terminal SH2 (NSH2) domains of phosphati-dylinositol3-kinase (PI-3K) binding subunit (p85) and Ras GTPase activating protein (GAP) in amounts
more &raquo; ... suitable for structure-function studies. The p85NSH2 domain stains dark purple and absorbs around 620-640 nm with Stains-all, a dye known to bind to calcium binding proteins. This effect was not observed for the GAPNSH2 domain. Circular dichroism analysis of the N-terminal SH2 domain of these proteins shows that p85NSH2, but not GAPNSH2, undergoes a significant dose-dependent change in conformation in the presence of increasing calcium concentrations. Moreover, the conformational change of p85NSH2 induced by calcium could be replicated by addition of a phosphorylated hexapeptide (DYpMDMK) representing the a-PDGFR binding site for p85. Limited proteolysis studies showed a significant calciumdependent increase in protection of p85NSH2 but not GAPNSH2 from degradation by subtilisin. Our results further indicate that holmium, a trivalent lanthanide ion, which has been previously shown to substitute for calcium, could also protect the p85NSH2 domain from proteolysis even at 10-fold lower concentrations. In uitro binding studies using purified preparations of activated a-PDGFR show that calcium did not affect the binding of GAPNSH2 domains to activated a-PDGFR. In striking contrast, we observed a marked increase in binding of p85NSH2 domains to activated a-PDGFR in the presence of calcium ions. Sequence * Corresponding author. Telephone (301) 496-9464. FAX (301) 496-Q Abstract published in Advance ACS Abstracts, December 15,1993. Abbreviations: PI-3K, phosphatidylinositol 3-kinase; GAP, GTPase activating protein; SH2, src-homology region 2; PDGF, platelet-derived growth factor; PDGFR, platelet-derived growth factor receptor; EGF, epidermal growth factor; EGFR, epidermal growth factor receptor; PLC" phospholipase C,; CD, circular dichroism; KI, kinase insert; NMR, nuclear magnetic resonance. 0 1994 American Chemical Societv Calcium-Dependent Binding of the NHSZ Domain of PI-3K to a-PDGFR
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/bi00169a016">doi:10.1021/bi00169a016</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/8292602">pmid:8292602</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2meymuyc65fajf4vdhd2lr4a4y">fatcat:2meymuyc65fajf4vdhd2lr4a4y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190221010503/http://pdfs.semanticscholar.org/2ae2/ee86906cb266bcae28dcf113f33400f3472e.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/2a/e2/2ae2ee86906cb266bcae28dcf113f33400f3472e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/bi00169a016"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acs.org </button> </a>

CDD: conserved domains and protein three-dimensional structure

Aron Marchler-Bauer, Chanjuan Zheng, Farideh Chitsaz, Myra K. Derbyshire, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu, Shennan Lu (+6 others)
<span title="2012-11-28">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
CDD, the Conserved Domain Database, is part of NCBI's Entrez query and retrieval system and is also accessible via http://www.ncbi.nlm.nih.gov/ Structure/cdd/cdd.shtml. CDD provides annotation of protein sequences with the location of conserved domain footprints and functional sites inferred from these footprints. Pre-computed annotation is available via Entrez, and interactive search services accept single protein or nucleotide queries, as well as batch submissions of protein query sequences,
more &raquo; ... tilizing RPS-BLAST to rapidly identify putative matches. CDD incorporates several protein domain and full-length protein model collections, and maintains an active curation effort that aims at providing fine grained classifications for major and wellcharacterized protein domain families, as supported by available protein three-dimensional (3D) structure and the published literature. To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks1243">doi:10.1093/nar/gks1243</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23197659">pmid:23197659</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3531192/">pmcid:PMC3531192</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kyfhbmseffcrjpuj7ie33t7trq">fatcat:kyfhbmseffcrjpuj7ie33t7trq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224062853/http://pdfs.semanticscholar.org/5dc7/237f225f72fcbca8cef7bcb83591a14608a1.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/5d/c7/5dc7237f225f72fcbca8cef7bcb83591a14608a1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks1243"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531192" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Crystal structure of a complex of HIV-1 protease with a dihydroxyethylene-containing inhibitor: Comparisons with molecular modeling

Narmada Thanki, J.K. Mohana Rao, Stephen I. Foundling, Alexander Wlodawer, W. Jeffrey Howe, Joseph B. Moon, John O. Hui, Alfredo G. Tomasselli, Robert L. Heinrikson, Suvit Thaisrivongs
<span title="">1992</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bubxfqklvdwthsc43yvjbtjae" style="color: black;">Protein Science</a> </i> &nbsp;
Thanki et al. Fig. 4 . 4 Stereo views of the superpositions of the modeled inhibitor (darker lines) and the X-ray crystal structure (thin lines). A: Original model.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pro.5560010811">doi:10.1002/pro.5560010811</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/1304383">pmid:1304383</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2142164/">pmcid:PMC2142164</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/phsylh73ofhbbljrpqpv7pd67y">fatcat:phsylh73ofhbbljrpqpv7pd67y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191122070255/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2142164&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/a1/e2/a1e2c44f5ee78af479b5ae3fab4f305b54d31281.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pro.5560010811"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2142164" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CDD: NCBI's conserved domain database

Aron Marchler-Bauer, Myra K. Derbyshire, Noreen R. Gonzales, Shennan Lu, Farideh Chitsaz, Lewis Y. Geer, Renata C. Geer, Jane He, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu (+8 others)
<span title="2014-11-20">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
NCBI's CDD, the Conserved Domain Database, enters its 15 th year as a public resource for the annotation of proteins with the location of conserved domain footprints. Going forward, we strive to improve the coverage and consistency of domain annotation provided by CDD. We maintain a live search system as well as an archive of pre-computed domain annotation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequences or in bulk. We also maintain import
more &raquo; ... edures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort. The curation effort aims at increasing coverage and providing finergrained classifications of common protein domains, for which a wealth of functional and structural data has become available. CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features. CDD can be accessed at http://www.ncbi.nlm.nih.gov/Structure/ cdd/cdd.shtml.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku1221">doi:10.1093/nar/gku1221</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25414356">pmid:25414356</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4383992/">pmcid:PMC4383992</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fmwggydorjhetcwv6griivaci4">fatcat:fmwggydorjhetcwv6griivaci4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302071633/http://pdfs.semanticscholar.org/9f5a/4be7eb1a3e405b2a2b97ecc47c2b97d42e4b.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/9f/5a/9f5a4be7eb1a3e405b2a2b97ecc47c2b97d42e4b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku1221"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383992" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Divalent Metal Ion Binding Site in the Kinase Insert Domain of the .alpha.-Platelet-Derived Growth Factor Receptor Regulates Its Association with SH2 Domains

Daruka Mahadevan, Narmada Thanki, Pilar Aroca, Peter McPhie, Jin-Chen Yu, John Beeler, Eugenio Santos, Alexander Wlodawer, Mohammad Heidaran
<span title="">1995</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4qyryvw5mvde5nt6xjruewxve4" style="color: black;">Biochemistry</a> </i> &nbsp;
To investigate the effects of metal ion binding to the a-PDGFR kinase insert domain, a PCR product representing amino acid residues 691 -795 (104 amino acids) was bacterially expressed and purified. Secondary structure prediction and circular dichroism spectroscopy indicated this domain to be a mixed a+p protein with a large coil/turn contribution. This 16 kDa, soluble, nonphosphorylated domain bound to 45Ca2+ and 65Zn2+ through a common shared site. Of the unlabeled divalent and trivalent
more &raquo; ... ions tested, Ho3+ = Zn2+ > Ni2+ > Ca2+ = Mn2+ > Mg2+, Ba2+ in competing for 45Ca2+ binding to this domain. In the presence of Ca2+ ions, the conformation of the KI domain changed significantly, and this changed conformation was resistant to subtilisin proteolysis. However, in the presence of Zn2+ ions, the conformation of the KI domain changed only slightly. Nevertheless, Zn2+ ions were more effective in rendering the KI domain resistant to proteolysis as compared to that shown by Ca2+ ions. In vitro binding studies using purified baculovirus-expressed a-PDGFR showed a marked increase in binding the p85 N-SH2 domain in the presence of Ca2+ or Zn2+ ions (KD = 0.5 pM), suggesting that metal ion binding enhances association of the p85 N-SH2 domain with the receptor. To confirm this, association of the a-PDGFR with the p85 N-SH2 domain was tested in the presence of the KI domain. The nonphosphorylated KI domain was effective in competing with the a-PDGFR for the binding of the p85 N-SH2 domain. This effect was more pronounced in the presence of Ca2+ ions. Microinjection of this domain into Xenopus oocytes delayed maturation in the presence of insulin but not progesterone. This suggests that the KI domain has a correctly folded three-dimensional structure compatible with biological activity. Together these findings indicate that the recombinant a-PDGFR KI domain binds the p85 N-SH2 domain and this binding is modulated by the presence of a novel divalent metal ion binding site within its structure. Abstract published in Advance ACS Abstracts, January 15, 1995. Abbreviations: PI-3K, phosphatidylinositol 3-kinase; a-PDGFR, a-platelet-derived growth factor receptor; KI, kinase insert; SH2, Srchomology region 2; CSF-lR, colony stimulating factor-1 receptor; GAP, GTPase activating protein; IRS-1, insulin receptor substrate-1; CD, circular dichroism. 496-8479. Institute.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/bi00007a002">doi:10.1021/bi00007a002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/7857921">pmid:7857921</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mg7mzpq6sfeinnyfg6on2uq7my">fatcat:mg7mzpq6sfeinnyfg6on2uq7my</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302215625/http://pdfs.semanticscholar.org/aa4f/563cef809162d9d14bd1b352183ae589adac.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/aa/4f/aa4f563cef809162d9d14bd1b352183ae589adac.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/bi00007a002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acs.org </button> </a>

Structural Role of Extracellular Domain 1 of α-Platelet-derived Growth Factor (PDGF) Receptor for PDGF-AA and PDGF-BB Binding

Daruka Mahadevan, Jin-Chen Yu, Jose W. Saldanha, Narmada Thanki, Peter McPhie, Aykut Uren, William J. LaRochelle, Mohammad A. Heidaran
<span title="1995-11-17">1995</span> <i title="American Society for Biochemistry &amp; Molecular Biology (ASBMB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mryncoafc5cxdicldzfm4vlsze" style="color: black;">Journal of Biological Chemistry</a> </i> &nbsp;
The purpose of this study was to bacterially express, purify, and refold combinations of the extracellular immunoglobulin (Ig)-like domains (2-3, 1-3, and 1-5) of the human ␣-platelet-derived growth factor receptor (␣PDGFR) to characterize molecular interactions with its ligand, platelet-derived growth factor (PDGF). The far UV circular dichroism spectroscopy of the ␣-PDGFR extracellular domains (ECDs) revealed a predominantly ␤-sheet protein, with a structure consistent with folded Ig-like
more &raquo; ... ins. The addition of PDGF-BB to these ECD types changed the conformation of all three types with a decrease in mean residue ellipticity in the following rank order: 1-5 ‫؍‬ 1-3 > 2-3. In striking contrast, addition of PDGF-AA to these ECD types markedly changed the conformation of ECD 2-3, by an increased mean residue ellipticity but no changes were observed for ECDs 1-3 and 1-5. PDGF-AA bound to the immobilized ECD types 2-3, 1-3, and 1-5 at concentrations of 20, 11, and 7.5 nM, respectively. In contrast, PDGF-BB bound the ECD types 2-3, 1-3, and 1-5 at concentrations of 3, 3, and 2.2 nM, respectively. Scatchard analysis of binding studies using labeled ECDs indicated that PDGF-BB bound ECD 1-3 and ECD 2-3 with K D values of 74 and 72 nM, respectively. While, PDGF-AA bound ECD 1-3 and ECD 2-3 with K D values of 33 and 87 nM, respectively. Therefore, our results indicated that the loss of ECD 1 impaired the binding affinity of ␣PDGFR ECD 1-3 toward PDGF-AA without having a similar effect on PDGF-BB binding. Together all of our data suggest that ECD 1 is differentially required for proper orientation of PDGF-AA but not PDGF-BB binding determinant within ECDs 2 and 3.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/jbc.270.46.27595">doi:10.1074/jbc.270.46.27595</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/7499222">pmid:7499222</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3it2jepv3bhmpcw7avjltcfc6q">fatcat:3it2jepv3bhmpcw7avjltcfc6q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426151841/http://www.jbc.org/content/270/46/27595.full.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/e8/ab/e8abccd9a3086ebdc5025b887ba8619bafd421c1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/jbc.270.46.27595"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

RefSeq: an update on prokaryotic genome annotation and curation

Daniel H Haft, Michael DiCuccio, Azat Badretdin, Vyacheslav Brover, Vyacheslav Chetvernin, Kathleen O'Neill, Wenjun Li, Farideh Chitsaz, Myra K Derbyshire, Noreen R Gonzales, Marc Gwadz, Fu Lu (+9 others)
<span title="2017-11-03">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) provides annotation for over 95 000 prokaryotic genomes that meet standards for sequence quality, completeness, and freedom from contamination. Genomes are annotated by a single Prokaryotic Genome Annotation Pipeline (PGAP) to provide users with a resource that is as consistent and accurate as possible. Notable recent changes include the development of a hierarchical evidence scheme, a new focus
more &raquo; ... n curating annotation evidence sources, the addition and curation of protein profile hidden Markov models (HMMs), release of an updated pipeline (PGAP-4), and comprehensive re-annotation of RefSeq prokaryotic genomes. Antimicrobial resistance proteins have been reannotated comprehensively, improved structural annotation of insertion sequence transposases and selenoproteins is provided, curated complex domain architectures have given upgraded names to millions of multidomain proteins, and we introduce a new kind of annotation rule--BlastRules. Continual curation of supporting evidence, and propagation of improved names onto RefSeq proteins ensures that the functional annotation of genomes is kept current. An increasing share of our annotation now derives from HMMs and other sets of annotation rules that are portable by nature, and available for download and for reuse by other investigators. RefSeq is found at https://www.ncbi.nlm.nih.gov/refseq/.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx1068">doi:10.1093/nar/gkx1068</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29112715">pmid:29112715</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5753331/">pmcid:PMC5753331</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hgvzb5wly5flvfsj7wlev6myby">fatcat:hgvzb5wly5flvfsj7wlev6myby</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223162559/http://pdfs.semanticscholar.org/52a8/c35b5587f9f8d76dc1ab392b823da7449880.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/52/a8/52a8c35b5587f9f8d76dc1ab392b823da7449880.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx1068"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753331" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

Aron Marchler-Bauer, Yu Bo, Lianyi Han, Jane He, Christopher J. Lanczycki, Shennan Lu, Farideh Chitsaz, Myra K. Derbyshire, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz (+10 others)
<span title="2016-11-29">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
NCBI's Conserved Domain Database (CDD) aims at annotating biomolecular sequences with the location of evolutionarily conserved protein domain footprints, and functional sites inferred from such footprints. An archive of pre-computed domain annotation is maintained for proteins tracked by NCBI's Entrez database, and live search services are offered as well. CDD curation staff supplements a comprehensive collection of protein domain and protein family models, which have been imported from
more &raquo; ... providers, with representations of selected domain families that are curated in-house and organized into hierarchical classifications of functionally distinct families and sub-families. CDD also supports comparative analyses of protein families via conserved domain architectures, and a recent curation effort focuses on providing functional characterizations of distinct subfamily architectures using SPARCLE: Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi. nlm.nih.gov/Structure/cdd/cdd.shtml.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw1129">doi:10.1093/nar/gkw1129</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27899674">pmid:27899674</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5210587/">pmcid:PMC5210587</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uwnork4w2bfhrovmauui7o5ejm">fatcat:uwnork4w2bfhrovmauui7o5ejm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223210719/http://pdfs.semanticscholar.org/5699/794ad396a965dc382e9e9e8dacc9ddd7fd2b.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/56/99/5699794ad396a965dc382e9e9e8dacc9ddd7fd2b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw1129"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210587" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The InterPro protein families and domains database: 20 years on

Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna Richardson, Gustavo A Salazar (+21 others)
<span title="2020-11-06">2020</span> <i title="Oxford University Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. InterProScan is the underlying software that allows protein and nucleic acid sequences to be searched against InterPro's signatures. Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases. InterPro combines signatures representing
more &raquo; ... ivalent families, domains or sites, and provides additional information such as descriptions, literature references and Gene Ontology (GO) terms, to produce a comprehensive resource for protein classification. Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation. Here, we report the status of InterPro (version 81.0) in its 20th year of operation, and its associated software, including updates to database content, the release of a new website and REST API, and performance improvements in InterProScan.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa977">doi:10.1093/nar/gkaa977</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33156333">pmid:33156333</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7778928/">pmcid:PMC7778928</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vfs7k3dxr5bcpbpvxbptj6r46m">fatcat:vfs7k3dxr5bcpbpvxbptj6r46m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210427095413/https://discovery.ucl.ac.uk/id/eprint/10115192/1/gkaa977.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/b7/47/b74764d7ba701d38149f71242600058a111ef1b7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa977"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778928" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

Alex L Mitchell, Teresa K Attwood, Patricia C Babbitt, Matthias Blum, Peer Bork, Alan Bridge, Shoshana D Brown, Hsin-Yu Chang, Sara El-Gebali, Matthew I Fraser, Julian Gough, David R Haft (+30 others)
<span title="2018-11-06">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky1100">doi:10.1093/nar/gky1100</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30398656">pmid:30398656</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ccbjkaabarhazk3yclk2vjjqoq">fatcat:ccbjkaabarhazk3yclk2vjjqoq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223065318/http://pdfs.semanticscholar.org/4116/2bda21503e284f5be64d1a02bf68d6e65ff8.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/41/16/41162bda21503e284f5be64d1a02bf68d6e65ff8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky1100"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a>

InterPro in 2017—beyond protein family and domain annotations

Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft (+35 others)
<span title="2016-11-29">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against Inter-Pro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, in-cluding the addition of two new databases
more &raquo; ... D and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by In-terPro, increase the overall number of residues annotated and allow more specific functional inferences.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw1107">doi:10.1093/nar/gkw1107</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27899635">pmid:27899635</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5210578/">pmcid:PMC5210578</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wa7z5pgpuffnrh5bf5ycimw7kq">fatcat:wa7z5pgpuffnrh5bf5ycimw7kq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501233042/http://udspace.udel.edu/bitstream/handle/19716/21353/InterPro%20in%202017%20beyond%20protein%20family%20and%20domain%20annotations_1492792560T0699.pdf;jsessionid=B665127B9705876C279C9E8BC8E6E152?sequence=1" 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/02/32/023201ee6bb05e9d602d56ac5620db60849af1a4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw1107"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210578" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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