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Predicting kinase inhibitors using bioactivity matrix derived informer sets

Huikun Zhang, Spencer S. Ericksen, Ching-pei Lee, Gene E. Ananiev, Nathan Wlodarchak, Peng Yu, Julie C. Mitchell, Anthony Gitter, Stephen J. Wright, F. Michael Hoffmann, Scott A. Wildman, Michael A. Newton (+1 others)
<span title="2019-08-05">2019</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
We develop this Informer-Based-Ranking (IBR) approach using the Published Kinase Inhibitor Sets (PKIS) as the chemogenomic data to select the informer sets.  ...  We compare different ways of using chemogenomic data to choose a small informer set of compounds based on previously measured bioactivity data.  ...  All baseline outcomes are shown in S4 Predicting kinase inhibitors using bioactivity matrix derived informer sets Another key characteristic of robust virtual screening performance is the recognition of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1006813">doi:10.1371/journal.pcbi.1006813</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31381559">pmid:31381559</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6695194/">pmcid:PMC6695194</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mmblevp77nbbzkqcn3sjxpghxy">fatcat:mmblevp77nbbzkqcn3sjxpghxy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191214190722/https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006813&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/ee/8a/ee8a550d5c0f9e0b22b09ea7cf366983174c8570.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1006813"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6695194" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Predicting kinase inhibitors using bioactivity matrix derived informer sets [article]

Huikun Zhang, Spencer S Ericksen, Ching-pei Lee, Gene E Ananiev, Nathan Wlodarchak, Julie C. Mitchell, Anthony Gitter, Stephen J Wright, F. Michael Hoffmann, Scott A. Wildman, Michael A Newton
<span title="2019-01-28">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We develop this Informer-Based-Ranking (IBR) approach using the Published Kinase Inhibitor Sets (PKIS) as the chemogenomic data to select the informer sets.  ...  We compare different ways of using chemogenomic data to choose a small informer set of compounds based on previously measured bioactivity data.  ...  ) kinase inhibitors as observed from the compound 654 bioactivity matrix.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/532762">doi:10.1101/532762</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/imfc7jegebchfa4vjd5x4dgy6e">fatcat:imfc7jegebchfa4vjd5x4dgy6e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501030009/https://www.biorxiv.org/content/biorxiv/early/2019/01/28/532762.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/7a/74/7a74d2127bfb59e85c71ffe74e1ab7c99a7abb42.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/532762"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors

Anna Cichonska, Balaguru Ravikumar, Elina Parri, Sanna Timonen, Tapio Pahikkala, Antti Airola, Krister Wennerberg, Juho Rousu, Tero Aittokallio, Avner Schlessinger
<span title="2017-08-07">2017</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
To evaluate its performance, we first predicted unmeasured binding affinities in a large-scale kinase inhibitor profiling study, and then experimentally tested 100 compound-kinase pairs.  ...  As a specific case study, we used tivozanib, an investigational VEGF receptor inhibitor with currently unknown off-target profile.  ...  With the optimized model, we predicted the bioactivity of tivozanib against the set of 138 kinases (S3 Table) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1005678">doi:10.1371/journal.pcbi.1005678</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28787438">pmid:28787438</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5560747/">pmcid:PMC5560747</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yfmm5krapveczelik4nz2b67fe">fatcat:yfmm5krapveczelik4nz2b67fe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426133522/https://helda.helsinki.fi/bitstream/handle/10138/214423/file.pdf;jsessionid=60778C9AD0C2A9D5CF85FC55A68ED62E?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/71/8a/718a0a9b110a01ecc90f89e8655559be452e3bcc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1005678"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5560747" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects

Isidro Cortés-Ciriano, Qurrat Ul Ain, Vigneshwari Subramanian, Eelke B. Lenselink, Oscar Méndez-Lucio, Adriaan P. IJzerman, Gerd Wohlfahrt, Peteris Prusis, Thérèse E. Malliavin, Gerard J. P. van Westen, Andreas Bender
<span title="">2015</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lsafitxtdvgnvg6b5zivcvv7mu" style="color: black;">MedChemComm</a> </i> &nbsp;
Proteochemometric (PCM) modelling is a computational method to model the bioactivity of multiple ligands against multiple related protein targets simultaneously.  ...  ) and the bioactivity for the remaining 30% (test set) is predicted.  ...  The high predictive ability of the models should be considered nevertheless with caution as the degree of completeness of the bioactivity matrix used in the training was only 0.65%.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c4md00216d">doi:10.1039/c4md00216d</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kvf2cuib6fbjta4dferweweugm">fatcat:kvf2cuib6fbjta4dferweweugm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428004201/https://helda.helsinki.fi/bitstream/handle/10138/224664/c4md00216d.pdf;jsessionid=55DE282E6CC8BEA70E50CCAA2085EFD0?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/88/a2/88a275ec04959065b83c319c793960b0bb055839.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c4md00216d"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Are phylogenetic trees suitable for chemogenomics analyses of bioactivity data sets: the importance of shared active compounds and choosing a suitable data embedding method, as exemplified on Kinases

Shardul Paricharak, Tom Klenka, Martin Augustin, Umesh A Patel, Andreas Bender
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5aubiwi6v5beng6iqzj577kiaa" style="color: black;">Journal of Cheminformatics</a> </i> &nbsp;
Compounds were described by chemical features, which were used to represent kinases (i.e. each kinase had an active set of features and an inactive set).  ...  to explain kinase promiscuity and selectivity against inhibitors.  ...  An active set and an inactive set of compounds (same compounds at different assay concentrations were considered unique) was derived for every kinase with compounds inhibiting kinase activity by 50% or  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1758-2946-5-49">doi:10.1186/1758-2946-5-49</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24330772">pmid:24330772</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3900467/">pmcid:PMC3900467</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y6y2f4jkrvbufp2g63axqlpvaa">fatcat:y6y2f4jkrvbufp2g63axqlpvaa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922012931/https://jcheminf.springeropen.com/track/pdf/10.1186/1758-2946-5-49?site=jcheminf.springeropen.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/23/ae/23ae7ba7bbc0fd78345623e5b8145082230f0d38.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1758-2946-5-49"> <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/PMC3900467" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Descriptor-Based Profile Analysis of Kinase Inhibitors to Predict Inhibitory Activity and to Grasp Kinase Selectivity

Hyejin Park, Kyeung Kyu Kim, ChangHoon Kim, Jae-Min Shin, Kyoung Tai No
<span title="2013-09-20">2013</span> <i title="Korean Chemical Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qqmow7eh6jbt3jvnfcg2xz7y3q" style="color: black;">Bulletin of the Korean Chemical Society (Print)</a> </i> &nbsp;
Here, we studied kinase selectivity by generating predictive models and analyzing their descriptors by using kinase-profiling data.  ...  Although many attempts to predict the activity and selectivity of kinase inhibitors have been made, the issue of selectivity has not yet been resolved.  ...  protein kinases. 18 This database provides curated data sets comprising the ChEMBL SAR data derived from published literature.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5012/bkcs.2013.34.9.2680">doi:10.5012/bkcs.2013.34.9.2680</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hd445miogbdjpejz43y7uje6au">fatcat:hd445miogbdjpejz43y7uje6au</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170820152254/http://ocean.kisti.re.kr/downfile/volume/chemical/JCGMCS/2013/v34n9/JCGMCS_2013_v34n9_2680.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/be/9f/be9fdc40352e7067c3769d5cd97108c0215e224b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5012/bkcs.2013.34.9.2680"> <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>

Predicting JNK1 Inhibitors Regulating Autophagy in Cancer using Random Forest Classifier [article]

Chetna Kumari, Naidu Subbarao, Muhammad Abulaish
<span title="2018-11-01">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Although limited informations are available to explore computational approaches to predict JNK1 inhibitors, it seems diificult to find literature exploring machine learning techniques to predict JNKs inhibitors  ...  This study aims to apply machine learning to predict JNK1 inhibitors regulating autophagy in cancer using Random Forest (RF).  ...  To date, limited informations are available with focus on computational studies to design JNKs inhibitors, while it is diificult to find literatures on prediction of isoform-specific JNKs inhibitors using  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/459669">doi:10.1101/459669</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6o7aos2menhuzmu6e6wfy53tlu">fatcat:6o7aos2menhuzmu6e6wfy53tlu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200324120602/https://www.biorxiv.org/content/biorxiv/early/2018/11/01/459669.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/29/c1/29c123334eef90119f7cbe96b252a0af377a26b6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/459669"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Linear Regression QSAR Models for Polo-Like Kinase-1 Inhibitors

Pablo Duchowicz
<span title="2018-02-14">2018</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3iichab3fbz7jq46o55l6trkq" style="color: black;">Cells</a> </i> &nbsp;
A structurally diverse dataset of 530 polo-like kinase-1 (PLK1) inhibitors is compiled from the ChEMBL database and studied by means of a conformation-independent quantitative structure-activity relationship  ...  The balanced subsets method partitions the dataset into training, validation, and test sets.  ...  The training set was used to calibrate the model and to obtain its parameters through the RM technique, while the validation set helped to calibrate and partially validate the model by predicting the bioactivity  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cells7020013">doi:10.3390/cells7020013</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29443884">pmid:29443884</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5850101/">pmcid:PMC5850101</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dsl6avlvyvejbf27qt7iux3js4">fatcat:dsl6avlvyvejbf27qt7iux3js4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180725022150/https://res.mdpi.com/def5020002a11b960e76695308b51210b42ccb8f780ba3626029ecfa46a714c2beaaa05ff1e8311181a305d201d6f8e77674f904a4d6e435cb4579c1848886b1a885639b05da7a85622b1c1d54b29edd8c8848857a8f85e83dd0645a39aa51ab3e60091c6e2370103d546276a9c95160d66b59d2a1f821b4ebf5bd81e943d3889d0cfab0591a6c3a50ab?filename=&amp;attachment=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/20/df/20df8610c9daf3652a1dc3e3f5b969a98f59768b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cells7020013"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850101" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

GSVM-Based Proteochemometrics Modeling for Prediction of Kinase-inhibitor Interaction

Yiqi Wang, Qingfeng Chen, Chaohong Wang, Yan Liang
<span title="2016-10-31">2016</span> <i title="Science and Engineering Research Support Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ipzxul43l5gzra2ybnqv2nfjpe" style="color: black;">International Journal of Control and Automation</a> </i> &nbsp;
Use of multi-targeted mining that select inhibitors act on a group of kinases increases the chance to achieve clinical antitumor activity.  ...  Proteochemometrics is a novel technology to predict inhibitor-kinase interactions from the chemical properties of kinase inhibitors which can help design more selective treatment and show better curative  ...  The kinase-inhibitor pairs whose kinases' subfamily is TKL are used as training set.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14257/ijca.2016.9.10.11">doi:10.14257/ijca.2016.9.10.11</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jcc36ffppverri5gdwvwrerrna">fatcat:jcc36ffppverri5gdwvwrerrna</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180602041430/http://www.sersc.org/journals/IJCA/vol9_no10/11.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/9e/f2/9ef2a35c8eabbe91d8fe5746c3015b8fe63c2490.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14257/ijca.2016.9.10.11"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Structure-Based Discovery and Bioactivity Evaluation of Novel Aurora-A Kinase Inhibitors as Anticancer Agents via Docking-Based Comparative Intermolecular Contacts Analysis (dbCICA)

Majd S. Hijjawi, Reem Fawaz Abutayeh, Mutasem O. Taha
<span title="2020-12-18">2020</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dstyyzbt45gknhqqjsh45p55h4" style="color: black;">Molecules</a> </i> &nbsp;
Aurora-A kinase inhibitors to specify the best possible docking settings needed to fit into the active-site binding pocket of Aurora-A kinase crystal structure, in a process that only potent ligands contact  ...  A fluorescence resonance energy transfer (FRET)-based assay was used to assess the activity of captured molecules and five promising Aurora-A kinase inhibitors were identified.  ...  The process of hits request was done in accordance with the predicted activity of (SB-1) model (i.e., whose settings were used as the 3D search query derived pharmacophore Refined-Hypo(SB-1), and after  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/molecules25246003">doi:10.3390/molecules25246003</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33353031">pmid:33353031</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2tr5se2wd5e7hclhltwb3ne5v4">fatcat:2tr5se2wd5e7hclhltwb3ne5v4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201224011127/https://res.mdpi.com/d_attachment/molecules/molecules-25-06003/article_deploy/molecules-25-06003.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/49/69/49693472c77d74917b6c7a20efc5a9f3e3bbc28c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/molecules25246003"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a>

Protein domain-based prediction of drug/compound–target interactions and experimental validation on LIM kinases

Tunca Doğan, Ece Akhan Güzelcan, Marcus Baumann, Altay Koyas, Heval Atas, Ian R. Baxendale, Maria Martin, Rengul Cetin-Atalay, Feixiong Cheng
<span title="2021-11-29">2021</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
DRUIDom is experimentally validated by syntheses and bioactivity analyses of compounds predicted to target LIM-kinase proteins, which play critical roles in the regulation of cell motility, cell cycle  ...  Predictive approaches such as virtual screening have been used in drug discovery with the objective of reducing developmental time and costs.  ...  Cytotoxic bioactivities of predicted inhibitors (LIMKi-1,3) and LIMKi-2 derivatives on human cells. Table 3.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1009171">doi:10.1371/journal.pcbi.1009171</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34843456">pmid:34843456</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8659301/">pmcid:PMC8659301</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5yvxwtolfrejhl2v5r4nvzif6u">fatcat:5yvxwtolfrejhl2v5r4nvzif6u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220202022416/https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009171&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/0b/d6/0bd69ce703414db27906801c6bc879a51ff7bb9e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1009171"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8659301" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Construction of Quantitative Structure Activity Relationship (QSAR) Models to Predict Potency of Structurally Diversed Janus Kinase 2 Inhibitors

Saw Simeon, Nathjanan Jongkon
<span title="2019-12-01">2019</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dstyyzbt45gknhqqjsh45p55h4" style="color: black;">Molecules</a> </i> &nbsp;
Janus kinase 2 (JAK2) inhibitors represent a promising therapeutic class of anticancer agents against many myeloproliferative disorders.  ...  Bioactivity data on pIC 50 of 2229 JAK2 inhibitors were employed in the construction of quantitative structure-activity relationship (QSAR) models.  ...  of the those models to predict unknown bioactivity properties depends largely on the size of training sets.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/molecules24234393">doi:10.3390/molecules24234393</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31805692">pmid:31805692</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6930640/">pmcid:PMC6930640</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ulx7stk3nrawjkzyktxkcszrpe">fatcat:ulx7stk3nrawjkzyktxkcszrpe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209221237/https://res.mdpi.com/d_attachment/molecules/molecules-24-04393/article_deploy/molecules-24-04393-v2.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/17/13/1713c5cc8206eb3b70a085de499a1653a8412165.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/molecules24234393"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6930640" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery

Albert J. Kooistra, Márton Vass, Ross McGuire, Rob Leurs, Iwan J. P. de Esch, Gert Vriend, Stefan Verhoeven, Chris de Graaf
<span title="2018-02-14">2018</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/trwqpvosfjh7dfyyosfmzcuwfq" style="color: black;">ChemMedChem</a> </i> &nbsp;
Obtaint he aligneds tructures and comparet he binding modes of the molecule pairs of interest * Design as caffold hop based on the selected moleculep air and dock them into the desired protein kinase  ...  kinase inhibitors.  ...  KLIFS nodes:K LIFS contains kinase-ligand interaction information derived from over 3900 structures covering more than 270 different kinases in complex with % 2500 unique ligands (accessed August 2017)  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cmdc.201700754">doi:10.1002/cmdc.201700754</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29337438">pmid:29337438</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5900740/">pmcid:PMC5900740</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mzevb2aezjctlmcg7wkfudox34">fatcat:mzevb2aezjctlmcg7wkfudox34</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210103333/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5900740&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/5f/03/5f039913ba7d0d417e4428765d226d83bd022c76.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cmdc.201700754"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5900740" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Crowdsourced mapping of unexplored target space of kinase inhibitors

Anna Cichońska, Balaguru Ravikumar, Robert J. Allaway, Fangping Wan, Sungjoon Park, Olexandr Isayev, Shuya Li, Michael Mason, Andrew Lamb, Ziaurrehman Tanoli, Minji Jeon, Sunkyu Kim (+95 others)
<span title="2021-06-03">2021</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
Here, we carry out a crowdsourced benchmarking of predictive algorithms for kinase inhibitor potencies across multiple kinase families tested on unpublished bioactivity data.  ...  The open-source prediction algorithms together with the bioactivities between 95 compounds and 295 kinases provide a resource for benchmarking prediction algorithms and for extending the druggable kinome  ...  Acknowledgements The authors thank the IDG Kinase Data and Resource Generation Center for generating new sets of target activity data for the Challenge Rounds 1 and 2, Olle Hansson (FIMM) for technical  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-021-23165-1">doi:10.1038/s41467-021-23165-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34083538">pmid:34083538</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/otj4dir66bhahci4fj56ifbw5a">fatcat:otj4dir66bhahci4fj56ifbw5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718133435/https://www.nature.com/articles/s41467-021-23165-1.pdf?error=cookies_not_supported&amp;code=2b3924b2-fcf6-45ec-ad6c-9e464e338087" 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/b4/e6b48cc83ce4f5f21455076fade9945e141b4bfd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-021-23165-1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a>

In silico target fishing: Predicting biological targets from chemical structure

Jeremy L. Jenkins, Andreas Bender, John W. Davies
<span title="">2006</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6b7t23yr6ffophcymqusi2ilgm" style="color: black;">Drug Discovery Today : Technologies</a> </i> &nbsp;
In silico target fishing is an emerging technology that enables the prediction of biological targets of compounds on the basis of chemical structure by using information from increasingly available biologically  ...  Provides smiles, similarity, sub-and super-structure searches and bioactivity information of hits.  ...  kinase inhibitor selectivity [10] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ddtec.2006.12.008">doi:10.1016/j.ddtec.2006.12.008</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7p6uljq43balfmxczca7eb7joi">fatcat:7p6uljq43balfmxczca7eb7joi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100613113329/http://mleg.cse.sc.edu/edu/csce822/uploads/Main.ReadingList/DM_BioTargetPredict.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/65/d0/65d040467d86c422f6332b9726843d2de972c598.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ddtec.2006.12.008"> <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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