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HOMCOS: an updated server to search and model complex 3D structures

Takeshi Kawabata
<span title="2016-08-13">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/pwcu5srt7nafvasezofrdon6ai" style="color: black;">Journal of Structural and Functional Genomics</a> </i> &nbsp;
The HOMCOS server (http://homcos.pdbj.org) was updated for both searching and modeling the 3D complexes for all molecules in the PDB.  ...  Their binding relationships are stored in the database.  ...  Akira Kinjo and Kei Yura for supervising the project. We also thank Prof. Haruki Nakamura for critical reading of the manuscript and allowing us to use the address ''.pdb.org'' for our server.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10969-016-9208-y">doi:10.1007/s10969-016-9208-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27522608">pmid:27522608</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5274653/">pmcid:PMC5274653</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e2heq6x7unbjpblyrl463rdpim">fatcat:e2heq6x7unbjpblyrl463rdpim</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171011043748/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/373/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjEwMDcvczEwOTY5LTAxNi05MjA4LXkucGRm.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/e6/e0/e6e0df46181b429e9daed1b4fb35f262bd2e92e7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10969-016-9208-y"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5274653" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

ASDB: a resource for probing protein functions with small molecules

Zhihong Liu, Peng Ding, Xin Yan, Minghao Zheng, Huihao Zhou, Yuehua Xu, Yunfei Du, Qiong Gu, Jun Xu
<span title="2016-01-28">2016</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;
Identifying chemical probes or seeking scaffolds for a specific biological target is important for protein function studies.  ...  The database can be retrieved through text or structure query tools. ASDB collects 333 601 scaffolds, which are associated with 4368 targets.  ...  The second option is structure query, which allows a user to conduct full structure search, substructure searches, and 2D or 3D similarity searches.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btw055">doi:10.1093/bioinformatics/btw055</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26822210">pmid:26822210</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/c7lbzryiibdjvgfsawufu7xu5m">fatcat:c7lbzryiibdjvgfsawufu7xu5m</a> </span>
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NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

Subodh Kumar Mishra, Amit Kumar
<span title="">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query.  ...  A 3D structure visualization tool has also been included for 3D structure representation of ligands.  ...  Arpita Tawani for their help in preparing the manuscript, and designing the database pages.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baw002">doi:10.1093/database/baw002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26896846">pmid:26896846</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4761111/">pmcid:PMC4761111</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2wx4pdzvkzco3kvrrv35me2lgq">fatcat:2wx4pdzvkzco3kvrrv35me2lgq</a> </span>
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SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures

N. Nadzirin, E. J. Gardiner, P. Willett, P. J. Artymiuk, M. Firdaus-Raih
<span title="2012-05-09">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;
Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures  ...  The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the Genome Computing Centre of the Malaysia Genome Institute for providing the computational infrastructure. We thank Mohd Noor  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks401">doi:10.1093/nar/gks401</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22573174">pmid:22573174</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3394286/">pmcid:PMC3394286</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5qocd76jmbfjxc6dtoy3f7ne7m">fatcat:5qocd76jmbfjxc6dtoy3f7ne7m</a> </span>
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WebChemDB: An Integrated Chemical Database Retrieval System

Bo-Kyeng Hou, Eun-Joung Moon, Sung-Chul Moon, Hae-Jin Kim
<span title="2009-12-31">2009</span> <i title="Korea Genome Organization"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/acfgmfmleze4rfuugy66fpl4ky" style="color: black;">Genomics &amp; Informatics</a> </i> &nbsp;
The web services API also provides researchers with functionalities to programmatically manipulate, search, and analyze the data. Availability: The database is accessible at  ...  WebChemDB is an integrated chemical database retrieval system that provides access to over 8 million publicly available chemical structures, including related information on their biological activities  ...  Acknowledgments We thank Jimin Hwang for editing the manuscript. This project was supported by the Korean Ministry of Education, Science and Technology (MEST) under grant number 2009-0080141.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5808/gi.2009.7.4.212">doi:10.5808/gi.2009.7.4.212</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e76wfdrgzbc5tm445qmz2svtie">fatcat:e76wfdrgzbc5tm445qmz2svtie</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170706051855/http://ocean.kisti.re.kr/downfile/volume/kgo/OJCHBH/2009/v7n4/OJCHBH_2009_v7n4_212.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/fe/62/fe6201be89e5db592a60ec1ed731c6bee1b9f881.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5808/gi.2009.7.4.212"> <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>

A review of three-dimensional chemical structure retrieval systems

Peter Willett
<span title="">1992</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mgvnagfuwjddxbu2ryhv4mxcii" style="color: black;">Journal of Chemometrics</a> </i> &nbsp;
APPLICATIONS OF 3D SEARCHING The availability of effective and efficient techniques for searching databases of 3D structures provides new tools for the solution of chemical and biological problems.  ...  The same screens are used to characterize both the structures in the database and the query pharmacophores that are to be searched for in this database. 2.3.2.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cem.1180060602">doi:10.1002/cem.1180060602</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qacctiu6pvfa5aoqv3h2xhpht4">fatcat:qacctiu6pvfa5aoqv3h2xhpht4</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/details/sim_journal-of-chemometrics_november-december-1992_6_6/page/290" title="read fulltext microfilm" 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> Archive [Microfilm] <div class="menu fulltext-thumbnail"> <img src="https://archive.org/serve/sim_journal-of-chemometrics_november-december-1992_6_6/__ia_thumb.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cem.1180060602"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Chemical Similarity Networks for Drug Discovery [chapter]

Yu-Chen Lo, Jorge Z. Torres
<span title="2016-11-30">2016</span> <i title="InTech"> Special Topics in Drug Discovery </i> &nbsp;
Chemical similarity networks are an emerging area of interest in medicinal chemistry, chemical biology, and systems chemoinformatics that are currently being applied to drug target prediction, drug repurposing  ...  In this chapter, we discuss the network-based drug target identification and discovery framework called chemical similarity network analysis pull-down (CSNAP) and its applications.  ...  Once the query ligands and chemical search parameters have been defined, the CSNAP algorithm will search the ChEMBL compound activity database to identify structurally similar compounds for target inference  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/65106">doi:10.5772/65106</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4hmygfcwt5honi7u5maxjnqc4i">fatcat:4hmygfcwt5honi7u5maxjnqc4i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501193117/https://cdn.intechopen.com/pdfs/52373.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/ad/a1/ada10dbbc11d051753c041e7bbff38bddfc1d530.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/65106"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

MSDmotif: exploring protein sites and motifs

Adel Golovin, Kim Henrick
<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;
Results: We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database.  ...  Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated.  ...  The small 3D structure motifs definition were provided by Prof. James Milner-White University of Glasgow.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-312">doi:10.1186/1471-2105-9-312</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18637174">pmid:18637174</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2491636/">pmcid:PMC2491636</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7rg254btwbfn5bim6534z6hr4y">fatcat:7rg254btwbfn5bim6534z6hr4y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829010946/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-9-312?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/5d/77/5d770945e5da1c0d111c1b6410eebd5a710f764b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-312"> <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/PMC2491636" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

SIMCOMP/SUBCOMP: chemical structure search servers for network analyses

M. Hattori, N. Tanaka, M. Kanehisa, S. Goto
<span title="2010-05-11">2010</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;
for the chemical substructure search, where both servers provide links to the KEGG PATHWAY and BRITE databases.  ...  Here, we demonstrate two types of chemical structure search servers: SIMCOMP (http://www .genome.jp/tools/simcomp/) for the chemical similarity search and SUBCOMP (http://www.genome .jp/tools/subcomp/)  ...  ACKNOWLEDGEMENTS We thank Tomohiro Ohya and Yusuke Sugihara for helpful discussions on the graph isomorphism problem of chemical compounds. Conflict of interest statement. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq367">doi:10.1093/nar/gkq367</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20460463">pmid:20460463</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2896122/">pmcid:PMC2896122</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7occz6qrlvg7dm5osg5eyhw5u4">fatcat:7occz6qrlvg7dm5osg5eyhw5u4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220064944/http://pdfs.semanticscholar.org/2059/66842b6cf20c7095e5bb8d1b84bcf43c7ffa.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/20/59/205966842b6cf20c7095e5bb8d1b84bcf43c7ffa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq367"> <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/PMC2896122" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

ChemDB update full-text search and virtual chemical space

J. H. Chen, E. Linstead, S. J. Swamidass, D. Wang, P. Baldi
<span title="2007-06-28">2007</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;
ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs  ...  Recent developments include optimization of chemical structure (and substructure) retrieval algorithms, enabling full database searches in less than a second.  ...  We thank the laboratory of Dr Tsai for the tuberculosis drug discovery collaboration.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btm341">doi:10.1093/bioinformatics/btm341</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17599932">pmid:17599932</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dc4dx3plangmliqry5wyy4bace">fatcat:dc4dx3plangmliqry5wyy4bace</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20130124043019/http://bioinformatics.oxfordjournals.org:80/content/23/17/2348.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/c3/23/c323677587e595c185de2e78e86a502352314645.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btm341"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Searching for pharmacophoric patterns in databases of three-dimensional chemical structures

Peter Willett
<span title="">1995</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lml5dbm4jnfmjitqk6yu3nrfd4" style="color: black;">Journal of Molecular Recognition</a> </i> &nbsp;
techniques for databases of three-dimensional (3D) chemical structures.  ...  of similarity measures that could provide analogous facili- ties for searching 3D databases.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jmr.300080503">doi:10.1002/jmr.300080503</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/8619950">pmid:8619950</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zrw25m53obdyjp5posqipup26a">fatcat:zrw25m53obdyjp5posqipup26a</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/details/sim_journal-of-molecular-recognition-jmr_september-october-1995_8_5/page/290" title="read fulltext microfilm" 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> Archive [Microfilm] <div class="menu fulltext-thumbnail"> <img src="https://archive.org/serve/sim_journal-of-molecular-recognition-jmr_september-october-1995_8_5/__ia_thumb.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jmr.300080503"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

A computational protocol to fragment-based drug design at PDB scale

F Moriaud, T Henry, SA Adcock, AM Vorotynsev, L Martin, O Doppelt, AG De Brevern, F Delfaud
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p7iwk2qc5vd5vjzop4eetdwh7e" style="color: black;">Chemistry Central Journal</a> </i> &nbsp;
MED-SuMo is used to query and mine the Surface Chemical Functions surrounding the fragments, seeking similarities with the protein of interest.  ...  MED-SuMo uses the binding site of the target as a query to search either the whole PDB (or any corporate protein structure databank) for all the binding sites that display a local match with the query.  ...  MED-SuMo is used to query and mine the Surface Chemical Functions surrounding the fragments, seeking similarities with the protein of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-153x-2-s1-s6">doi:10.1186/1752-153x-2-s1-s6</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4236202/">pmcid:PMC4236202</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/743isgextzbqvglux4zes4w5fa">fatcat:743isgextzbqvglux4zes4w5fa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170820200259/https://ccj.springeropen.com/track/pdf/10.1186/1752-153X-2-S1-S6?site=ccj.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/1a/61/1a6174c51f46137cf01c29736af272bdf3afd7b4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-153x-2-s1-s6"> <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/PMC4236202" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

EnzyMine: a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature

Dandan Sun, Xingxiang Cheng, Yu Tian, Shaozhen Ding, Dachuan Zhang, Pengli Cai, Qian-nan Hu
<span title="2020-10-01">2020</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
Addition of chemical structural information in enzymatic reactions has proven to be significant for accurate enzyme function prediction.  ...  However, such chemical data lack systematic feature mining and hardly exist in enzyme-related databases.  ...  Figure 4 . 4 Detailed EnzyMine screenshot and search results for EC:1.1.1.1 are shown. (A) Front-end search methods based on text query and molecular searching query.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baaa065">doi:10.1093/database/baaa065</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33002112">pmid:33002112</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kcbu33zg4baenj5yrcrohclxqe">fatcat:kcbu33zg4baenj5yrcrohclxqe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201003014042/https://watermark.silverchair.com/baaa065.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAscwggLDBgkqhkiG9w0BBwagggK0MIICsAIBADCCAqkGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMO53OAAB1vgBQ379yAgEQgIICek26HVfWftDiiJYezXVyleP8CA3X2GzJiM4ulPN0Te6A1gegmWWHU9maafwgU9s37WKj55yFgNTI5_1apJkZA9m-QKnB9gxgV7hrPWjlCOMBqIzCo-cGrG-Vgos5icrgvofI6D8JHP3IBCoIA0ExmcQEYwFLzIqzzNNF_nCiLYwwzBI1gbzHscw62-_71I1jHwimLB5I2_MpglZhYxs6PuMspH8bmLqn7zW7N4TqZxu5epIgoA4wWuOl5yvSF2JzekGAjRwBeGvA_muB6AzjbFji-plxbvOOU7YnJ5XYpVDY_nJWX0nJmzUcjfHcXy1MtB1vhwIoKg5iLTBVUpeHWGIytZLWd7qzPVn2RyzeGUyNFs5G9a2CvnMQlmJACMj5ALtaY3vCDwDj1dCS8x2qyScN_HsHFDOJ1YxgeT9IY7tOy-Zo4BnPy5QYKgUSzjg27m906aboEAPZKpvaic3ezOrvkx4EaIQC-6rYHv0ug21A5cPFu_Kbej5r1iAKiyJscdP8Brd0Qym8MRssq-eY09S38SHhdkshfQ5y9q5E4QAGMvTShO2LQQOC7uC-jVWbv_CAzIDFOAqYDAdQ68P7mYL6EnGfodRjQNPHWFkmY8MHpekiH6mlDcWH85rNS5vXmOK7Oe9u1nHXYdjcDsd7CIWGVg1GjnJCgO4VJoP7OhR58zGvKA5ZV9p25_lC0D6lK5WRNI1Mwgq-gGdi6Lmr3HCPOGTApKleHFhaIjTbqQlNzv0EWFu-ij-Y6sFzvoxtBWBoB5-VaGSSOGlOrpGMxbfuCPnvIoV36GEa1RC9OuD9TfhcvATalCLikwCVP8YkjancrJJqW0bz0DA" 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/3a/2c/3a2cbf3463dfcca03588e7bbe80392a4e2b2b0ce.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baaa065"> <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>

SimilarityLab: Molecular Similarity for SAR Exploration and Target Prediction on the Web

Steven Shave, Manfred Auer
<span title="2021-08-27">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vt2hc3xcijfofb7cwnxv4hhszi" style="color: black;">Processes</a> </i> &nbsp;
In addition to searching for commercially available molecules similar to a query compound, SimilarityLab also enables the search of compounds with recorded activities, generating consensus counts of activities  ...  similarity measure, SimilarityLab's set of commercially available small molecules is consistently updated, currently containing over 12.7 million unique small molecules, and not relying on published databases  ...  Figure 3 . 3 SimilarityLab 2D drawing interface for 3D similarity searching, shown with the approved drug diclofenac being queried.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/pr9091520">doi:10.3390/pr9091520</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gywkuk2funfxbpbmgubph6tmq4">fatcat:gywkuk2funfxbpbmgubph6tmq4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210902073823/https://res.mdpi.com/d_attachment/processes/processes-09-01520/article_deploy/processes-09-01520.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/6d/bf/6dbfad724c2a6a31cb33dbb39299c89dc7a1cc86.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/pr9091520"> <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>

Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace

<span title="2020-03-18">2020</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
The interplay between life sciences and advancing technology drives a continuous cycle of chemical data growth; these data are most often stored in open or partially open databases.  ...  In parallel, many different types of algorithms are being developed to manipulate these chemical objects and associated bioactivity data.  ...  3D similarity search [17, 97] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbaa034">doi:10.1093/bib/bbaa034</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32187356">pmid:32187356</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7986591/">pmcid:PMC7986591</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mq3csvzjkfekhpjfti2wmyipxi">fatcat:mq3csvzjkfekhpjfti2wmyipxi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718180812/https://hal.archives-ouvertes.fr/hal-03246816/file/bbaa034.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/92/02/92021bcd4dbb66cb5ff7073551ca2cb7ad6acd51.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbaa034"> <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/PMC7986591" 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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