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A chemogenomics view on protein-ligand spaces

Helena Strömbergsson, Gerard J Kleywegt
<span title="">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Conclusion: In this study, we present an approach to visualize protein-ligand spaces from a chemogenomics perspective, where both ligand and protein features are taken into account.  ...  Protein and ligand space have previously been studied as separate entities, but chemogenomics studies deal with large datasets that cover parts of the joint protein-ligand space.  ...  Lars Liljas at the Department of Cell and Molecular Biology, Uppsala, for help with compiling a list of non-specific binding ligands in protein crystal structures. We are also very grateful to Drs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-10-s6-s13">doi:10.1186/1471-2105-10-s6-s13</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19534738">pmid:19534738</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2697636/">pmcid:PMC2697636</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a5xujvulxfg7hiw3egsinm345y">fatcat:a5xujvulxfg7hiw3egsinm345y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829005153/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-10-S6-S13?site=http://bmcbioinformatics.biomedcentral.com" 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/d9/26/d926efcfd1ad19076c47f6f950eac94bded1e55b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-10-s6-s13"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697636" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Chemogenomics Approaches for Receptor Deorphanization and Extensions of the Chemogenomics Concept to Phenotypic Space

Eelke van der Horst, Julio E. Peironcely, Gerard J. P. van Westen, Olaf O. van den Hoven, Warren R. J. D. Galloway, David R. Spring, Joerg K. Wegner, Herman W. T. van Vlijmen, Ad P. IJzerman, John P. Overington, Andreas Bender
<span title="2011-08-01">2011</span> <i title="Bentham Science Publishers Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/k222f4mitzcuhmu2nnbcda5dqa" style="color: black;">Current Topics in Medicinal Chemistry</a> </i> &nbsp;
Finally, we extend the concept of 'chemogenomics' approaches, relating ligand chemistry to bioactivity against related targets, into phenotypic space which then falls into the area of 'chemical genomics  ...  bioactive ligands can be inferred, we investigate the extent to which chemogenomics approaches can be applied to receptor deorphanization.  ...  One of the most comprehensive recent studies [28] was attempting to model all protein-ligand interaction space of enzymes, as taken from protein-ligand cocrystals.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/156802611796391230">doi:10.2174/156802611796391230</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21470175">pmid:21470175</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/f2cikalwdrfipci22wnuxrn7lu">fatcat:f2cikalwdrfipci22wnuxrn7lu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170813063413/http://juliopeironcely.com/wp-content/uploads/2011/06/2011_CTMC_ASAP.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/f5/b7/f5b7d21615f02b48f880e217fb7286ddb527cd58.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/156802611796391230"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Virtual screening of GPCRs: An in silico chemogenomics approach

Laurent Jacob, Brice Hoffmann, Véronique Stoven, Jean-Philippe Vert
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
on the biological space of targets and on the chemical space of small molecules.  ...  Conclusion: We propose new methods for in silico chemogenomics and validate them on the virtual screening of GPCRs.  ...  Because the protein-ligand recognition process occurs in 3D space in a pocket involving a limited number of residues, we tried to describe the GPCR space using a representation of this pocket.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-363">doi:10.1186/1471-2105-9-363</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18775075">pmid:18775075</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2553090/">pmcid:PMC2553090</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ykcsgo2owzhgdbjoqsdjqoifdm">fatcat:ykcsgo2owzhgdbjoqsdjqoifdm</a> </span>
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Chemogenomic approaches to rational drug design

D Rognan
<span title="">2007</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wsc2264oo5gpvk5scotezp75pu" style="color: black;">British Journal of Pharmacology</a> </i> &nbsp;
Chemogenomics is this emerging research field aimed at systematically studying the biological effect of a wide array of small molecular-weight ligands on a wide array of macromolecular targets.  ...  opens the way to global drug-discovery approaches, no more focused on a single target but on an entire family of related proteins or on a full metabolic pathway.  ...  be limited here in a tiny protein space.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/sj.bjp.0707307">doi:10.1038/sj.bjp.0707307</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17533416">pmid:17533416</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1978269/">pmcid:PMC1978269</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qpqd5ps65fgttnbgqesrjc2ml4">fatcat:qpqd5ps65fgttnbgqesrjc2ml4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20140514103431/http://bioinfo-pharma.u-strasbg.fr:80/labwebsite/publications/paper100.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/96/1b/961bc85aaa8856ecf49f9940f64ae4c2a868daf0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/sj.bjp.0707307"> <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/PMC1978269" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Active learning for computational chemogenomics

Daniel Reker, Petra Schneider, Gisbert Schneider, JB Brown
<span title="">2017</span> <i title="Future Science, LTD"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vj5onv5w7zeoxhg43x7xhqw6py" style="color: black;">Future Medicinal Chemistry</a> </i> &nbsp;
This might serve in part as an explanation why most computational chemogenomic applications have focused on specific subfamilies of proteins and ligands [40] .  ...  Commonly, chemogenomics approaches rely on concatenating descriptors for ligands and targets as inputs to statistical learning methods that classify a query ligand-target pair as interacting or noninteracting  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4155/fmc-2016-0197">doi:10.4155/fmc-2016-0197</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28263088">pmid:28263088</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pnzwd3jfsjcu3gpnnxmidq7tge">fatcat:pnzwd3jfsjcu3gpnnxmidq7tge</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722105613/https://www.research-collection.ethz.ch/bitstream/handle/20.500.11850/207556/fmc-2016-0197.pdf;jsessionid=73BC941999416B49A8B89688FEE90672?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/ba/0c/ba0c8ce1358bd713b3221bd9207223892cf09736.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4155/fmc-2016-0197"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Evaluation of deep and shallow learning methods in chemogenomics for the prediction of drugs specificity

Benoit Playe, Veronique Stoven
<span title="2020-02-10">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5aubiwi6v5beng6iqzj577kiaa" style="color: black;">Journal of Cheminformatics</a> </i> &nbsp;
Chemogenomics, also called proteochemometrics, covers a range of computational methods that can be used to predict protein-ligand interactions at large scales in the protein and chemical spaces.  ...  They differ from more classical ligand-based methods (also called QSAR) that predict ligands for a given protein receptor.  ...  Jacob and Vert [5] used the Kronecker product of protein and ligand kernels to define the kernel associated with the chemogenomic space, i.e. the space of (protein,molecule) pairs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13321-020-0413-0">doi:10.1186/s13321-020-0413-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33431042">pmid:33431042</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ynemzscg3bbspctby3dexzqi6e">fatcat:ynemzscg3bbspctby3dexzqi6e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200211100719/https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-0413-0" 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/e6/19/e619389048527e2e1a4369f9ae8268b23aea2a6b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13321-020-0413-0"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers

Y. Tabei, E. Pauwels, V. Stoven, K. Takemoto, Y. Yamanishi
<span title="2012-09-07">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
The extracted substructure-domain association network enables us to suggest ligand chemical fragments specific for each protein domain and ligand core substructures important for a wide range of protein  ...  We propose a novel algorithm for extracting informative chemogenomic features by using L 1 regularized classifiers over the tensor product space of possible drug-target pairs.  ...  Chemogenomics is an emerging research area that attempts to associate the chemical space of possible ligands with the genomic space of possible proteins (Dobson, 2004; Kanehisa et al., 2006; Stockwell  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts412">doi:10.1093/bioinformatics/bts412</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22962471">pmid:22962471</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3436839/">pmcid:PMC3436839</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7dgumrgpt5g5zc4by25z6ygpzu">fatcat:7dgumrgpt5g5zc4by25z6ygpzu</a> </span>
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Evaluation of network architecture and data augmentation methods for deep learning in chemogenomics [article]

Benoit Playe, Véronique Stoven
<span title="2019-06-06">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
, at at scales both in the protein and chemical spaces.  ...  and protein attribute views, instead of focusing on sophisticated, yet intuitively relevant, encoder's neuron network architecture.  ...  Indeed, we can formulate the problem of predicting DTIs at a large scale in the protein and molecule spaces as a problem of predicting ligands for each protein, while learning on all the problems of predicting  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/662098">doi:10.1101/662098</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zpms2rox2zbmhgbk4ktobedb2u">fatcat:zpms2rox2zbmhgbk4ktobedb2u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200324012453/https://www.biorxiv.org/content/biorxiv/early/2019/06/06/662098.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/ba/db/badbfa4be18d3f26a9fd4c3504b1af731c489988.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/662098"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Enhanced hit-to-lead process using bioanalogous lead evolution and chemogenomics: application in designing selective matrix metalloprotease inhibitors

Ákos Papp, Tamás Szommer, László Barna, Gergely Gyimesi, Péter Ferdinandy, Cesare Spadoni, Ferenc Darvas, Toshio Fujita, László Ürge, György Dormán
<span title="">2007</span> <i title="Informa Healthcare"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4m2squtugrdvtgjdvfbz5jhmaq" style="color: black;">Expert Opinion on Drug Discovery</a> </i> &nbsp;
The ligand space was then arranged into a lead evolution tree, where the substructural transformations in each virtual step led to marked changes in the activity pattern.  ...  The authors applied this method in the design of selective inhibitors of matrix metalloproteases (MMPs), also referred to as matrixins, on the basis of a unique analysis of the ligand-target knowledge  ...  Ligand-target chemogenomics knowledge space: the ligand-target matrix By its very nature, the effectiveness of the chemogenomics approach largely depends on the compilation of a detailed ligand-target  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1517/17460441.2.5.707">doi:10.1517/17460441.2.5.707</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23488960">pmid:23488960</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g2fzmagqabahhgyanunuvnuagi">fatcat:g2fzmagqabahhgyanunuvnuagi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110516151025/http://www.enzim.hu:80/~lbarna/articles/EODCPapp.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/59/e8/59e8997a349e8bedd0deed043342c5b392803f5d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1517/17460441.2.5.707"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Protein-ligand interaction prediction: an improved chemogenomics approach

Laurent Jacob, Jean-Philippe Vert
<span title="2008-08-01">2008</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Following the recent chemogenomics trend, we adopt a cross-target view and attempt to screen the chemical space against whole families of proteins simultaneously.  ...  Results: We propose a systematic method to predict ligand-protein interactions, even for targets with no known 3D structure and few or no known ligands.  ...  ACKNOWLEDGEMENTS We thank Pierre Mahé for his help with ChemCPP and kernels for molecules, and Véronique Stoven for insightful discussions on the biological aspects of the problem.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btn409">doi:10.1093/bioinformatics/btn409</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18676415">pmid:18676415</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2553441/">pmcid:PMC2553441</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lo7rjt7oyjee3lt6rwjwg2mcni">fatcat:lo7rjt7oyjee3lt6rwjwg2mcni</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170706034742/http://members.cbio.mines-paristech.fr/~jvert/svn/bibli/local/Jacob2008Protein.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/bd/21/bd211f543d78fccb1930d3a665cd81cc99643047.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btn409"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553441" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Systemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery

Maykel Cruz-Monteagudo, Stephan Schürer, Eduardo Tejera, Yunierkis Pérez-Castillo, José L. Medina-Franco, Aminael Sánchez-Rodríguez, Fernanda Borges
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q2rzh4rosrd2rhrlmpfocas4qa" style="color: black;">Drug Discovery Today</a> </i> &nbsp;
Here, we introduce a new concept, 'Systemic Chemogenomics/Quantitative Structure-Activity Relationship (QSAR)'. To elaborate on the concept, relevant information surrounding it is addressed.  ...  The concept is challenged by implementing a systemic QSAR approach for phenotypic virtual screening (VS) of candidate ligands acting as neuroprotective agents in Parkinson's disease (PD).  ...  The joint result is a disease-relevant chemogenomic space. iv. Target fishing of the ligands included in the disease-relevant chemogenomic space.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.drudis.2017.02.004">doi:10.1016/j.drudis.2017.02.004</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28274840">pmid:28274840</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5487293/">pmcid:PMC5487293</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ipsruox4zbas3dhcyqqwh25fei">fatcat:ipsruox4zbas3dhcyqqwh25fei</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191106010115/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5487293&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/e9/d7/e9d7a45e4252b7953b5261e0434e9eb64eba9659.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.drudis.2017.02.004"> <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/PMC5487293" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

One Drug for Multiple Targets: A Computational Perspective

Oscar Méndez-Lucio, J. Jesús Naveja, Hugo Vite-Caritino, Fernando Daniel Prieto-Martínez, José Luis Medina-Franco
<span title="2017-10-12">2017</span> <i title="Sociedad Quimica de Mexico, A.C."> Journal of the Mexican Chemical Society </i> &nbsp;
A survey of modern methodologies to design and develop multiple-target ligands is presented with a special focus on computational-based methods.  ...  Acknowledgments We thank the funding from the 'Programa de Apoyo a la Investigación y el Posgrado' (PAIP) 5000-9163, Facultad de Química, UNAM and from the program 'Nuevas Alternativas de Tratamiento para  ...  As a result, this technique allows the simultaneous navigation, inter-and extrapolation in both chemical space (i.e. ligands) and biological space (i.e. protein target) [70, 71] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.29356/jmcs.v60i3.100">doi:10.29356/jmcs.v60i3.100</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/khyfn3epo5ayzgkk4uxkd4p6k4">fatcat:khyfn3epo5ayzgkk4uxkd4p6k4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200306120646/https://www.jmcs.org.mx/index.php/jmcs/article/download/100/99" 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/f9/1f/f91fe30a22dcb56e462889513820a4e2aabf0c53.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.29356/jmcs.v60i3.100"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

A structural chemogenomics analysis of aminergic GPCRs: lessons for histamine receptor ligand design

A J Kooistra, S Kuhne, I J P de Esch, R Leurs, C de Graaf
<span title="2013-08-15">2013</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wsc2264oo5gpvk5scotezp75pu" style="color: black;">British Journal of Pharmacology</a> </i> &nbsp;
BACKGROUND AND PURPOSE Chemogenomics focuses on the discovery of new connections between chemical and biological space leading to the discovery of new protein targets and biologically active molecules.  ...  G-protein coupled receptors (GPCRs) are a particularly interesting protein family for chemogenomics studies because there is an overwhelming amount of ligand binding affinity data available.  ...  Based on the assumption that similar proteins bind similar ligands (and vice versa) knowledge on the molecular determinants of protein-ligand interactions can be used to identify novel ligands for a given  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/bph.12248">doi:10.1111/bph.12248</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23713847">pmid:23713847</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3764853/">pmcid:PMC3764853</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j4q5s2odz5gjpiw6idj5jwqpvq">fatcat:j4q5s2odz5gjpiw6idj5jwqpvq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206100014/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3764853&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/b5/8b/b58b5ea0d8b8605285c186b32af85130d997aa4e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/bph.12248"> <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/PMC3764853" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Efficient multi-task chemogenomics for drug specificity prediction

Benoit Playe, Chloé-Agathe Azencott, Véronique Stoven, Alexandre G. de Brevern
<span title="2018-10-04">2018</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
for the protein nor for the ligand.  ...  OPEN ACCESS Citation: Playe B, Azencott C-A, Stoven V (2018) Efficient multi-task chemogenomics for drug specificity prediction. PLoS ONE 13(10): e0204999. https://doi.org/10.  ...  Finally, chemogenomic approaches [8] can be viewed as an attempt to fill a large binary interaction matrix where rows are molecules and columns are proteins, partially filled with the known protein-ligand  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0204999">doi:10.1371/journal.pone.0204999</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x4vm7shktzhubhopz75cw7t4am">fatcat:x4vm7shktzhubhopz75cw7t4am</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191214051943/https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0204999&amp;type=printable" 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/43/a8/43a8966ed09beaf4d16c801d368771e38b02ae5a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0204999"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a>

Current computational methods for predicting protein interactions of natural products

Aurélien F.A. Moumbock, Jianyu Li, Pankaj Mishra, Mingjie Gao, Stefan Günther
<span title="2019-10-28">2019</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cmflnsn2l5gylcviv447te3mku" style="color: black;">Computational and Structural Biotechnology Journal</a> </i> &nbsp;
The prediction of their interaction profiles with druggable protein targets remains a major challenge in modern drug discovery.  ...  Natural products (NPs) are an indispensable source of drugs and they have a better coverage of the pharmacological space than synthetic compounds, owing to their high structural diversity.  ...  view, with a special focus on NPs, which have been and will continue to be an indispensable source of drugs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.csbj.2019.08.008">doi:10.1016/j.csbj.2019.08.008</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31762960">pmid:31762960</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6861622/">pmcid:PMC6861622</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ml6p54iqjvh5lh7nzew2xhm3oe">fatcat:ml6p54iqjvh5lh7nzew2xhm3oe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200501153858/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6861622&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/d7/32/d732e70f21ae7785bbf7643e5fc662d4cab7285d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.csbj.2019.08.008"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6861622" 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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