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PubChem3D: a new resource for scientists

Evan E Bolton, Jie Chen, Sunghwan Kim, Lianyi Han, Siqian He, Wenyao Shi, Vahan Simonyan, Yan Sun, Paul A Thiessen, Jiyao Wang, Bo Yu, Jian Zhang (+1 others)
<span title="">2011</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;
With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to  ...  A new layer called PubChem3D is added to PubChem to assist in this analysis.  ...  Authors' contributions All authors contributed in a material way to the PubChem3D project.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1758-2946-3-32">doi:10.1186/1758-2946-3-32</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21933373">pmid:21933373</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3269824/">pmcid:PMC3269824</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hehjmmenqrewfbujpowbze43ni">fatcat:hehjmmenqrewfbujpowbze43ni</a> </span>
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PubChem3D: conformer ensemble accuracy

Sunghwan Kim, Evan E Bolton, Stephen H Bryant
<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;
PubChem is a free and publicly available resource containing substance descriptions and their associated biological activity information.  ...  , found for PDB ligands.  ...  Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data [10] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1758-2946-5-1">doi:10.1186/1758-2946-5-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23289532">pmid:23289532</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3547714/">pmcid:PMC3547714</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iotioq35nbfehnqdb6pvhobniu">fatcat:iotioq35nbfehnqdb6pvhobniu</a> </span>
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PubChem3D: Diversity of shape

Evan E Bolton, Sunghwan Kim, Stephen H Bryant
<span title="">2011</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;
It was shown that a given volume was able to describe 40-70% of the shape diversity of lesser volumes, for the majority of the volume range considered in this study.  ...  The rate of growth in shape space, as represented by a decreasing shape similarity threshold, was found to be remarkably smooth as a function of volume.  ...  Acknowledgements We are grateful to the NCBI Systems staff, especially Ron Patterson, Charlie Cook, and Don Preuss, whose efforts helped make the PubChem3D project possible.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1758-2946-3-9">doi:10.1186/1758-2946-3-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21418625">pmid:21418625</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3072936/">pmcid:PMC3072936</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/royrziwopzgdjcmfhmjzwtwoae">fatcat:royrziwopzgdjcmfhmjzwtwoae</a> </span>
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Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis

Sunghwan Kim, Evan E Bolton, Stephen H Bryant
<span title="">2012</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;
Therefore, the efficient use of PubChem3D resources requires an understanding of the statistical and biological meaning of computed 3-D molecular similarity scores between molecules.  ...  Interestingly, the best-conformer-pair approach also increased the average 3-D similarity scores for the non-inactive-non-inactive (NN) pairs for a given assay, by comparable amounts to those for the random  ...  We are also thankful to the reviewers for their insightful suggestions and comments. SK thanks to Volker Hähnke for fruitful discussion on this study.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1758-2946-4-28">doi:10.1186/1758-2946-4-28</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23134593">pmid:23134593</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3537644/">pmcid:PMC3537644</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2tuor3wxtnbahkyaqkhd76yycq">fatcat:2tuor3wxtnbahkyaqkhd76yycq</a> </span>
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Drug Repurposing: A Paradigm Shift in Drug Discovery

Saravanan Jayaram, Emdormi Rymbai, Deepa Sugumar, Divakar Selvaraj
<span title="2020-06-30">2020</span> <i title="Sierra Journals"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ftrvoenf3fajvh4qshks3suphq" style="color: black;">International Journal of Applied Pharmaceutical Sciences and Research</a> </i> &nbsp;
Target identification, target validation; lead identification; and lead optimization are a lengthy and unreliable process that further complicates the discovery of new drugs.  ...  Therefore, an alternative to traditional drug discovery is drug repurposing, a process in which already existing drugs are repurposed for conditions other than which were originally intended.  ...  (DST-FIST), New Delhi for their infrastructure support to our department.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.21477/ijapsr.5.4.2">doi:10.21477/ijapsr.5.4.2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sif74lfnungnjhbtezcgiocuri">fatcat:sif74lfnungnjhbtezcgiocuri</a> </span>
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Semantic inference using chemogenomics data for drug discovery

Qian Zhu, Yuyin Sun, Sashikiran Challa, Ying Ding, Michael S Lajiness, David J Wild
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
We have previously described a tool called WENDI for aggregating information pertaining to new chemical compounds, effectively creating evidence paths relating the compounds to genes, diseases and so on  ...  Results Through the implementation of a semantic inference algorithm, rule set, Semantic Web methods (RDF, OWL and SPARQL) and new interfaces, we have created a new tool called Chemogenomic Explorer that  ...  We thank Bret Davidson for correcting English. We would like to thank the anonymous reviewers for their helpful comments and suggestions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-256">doi:10.1186/1471-2105-12-256</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21699718">pmid:21699718</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3225082/">pmcid:PMC3225082</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/udmnme6lzneytj3ruo5i7r46zy">fatcat:udmnme6lzneytj3ruo5i7r46zy</a> </span>
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