Pub Date : 2020-02-06DOI: 10.1089/cmb.2019.29024.zc
Zhipeng Cai, P. Skums, A. Zelikovsky
{"title":"Preface Special Issue: 15th International Symposium on Bioinformatics Research and Applications (ISBRA 2019)","authors":"Zhipeng Cai, P. Skums, A. Zelikovsky","doi":"10.1089/cmb.2019.29024.zc","DOIUrl":"https://doi.org/10.1089/cmb.2019.29024.zc","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"32 1","pages":"131-132"},"PeriodicalIF":0.0,"publicationDate":"2020-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77097048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-01-01DOI: 10.1504/IJCBDD.2020.113855
Xiuquan Wang, Keli Xu, Junqing Wang, Yunyun Zhou
{"title":"LCLE: a web portal for lncRNA network analysis in liver cancer","authors":"Xiuquan Wang, Keli Xu, Junqing Wang, Yunyun Zhou","doi":"10.1504/IJCBDD.2020.113855","DOIUrl":"https://doi.org/10.1504/IJCBDD.2020.113855","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"15 1","pages":"520-528"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78980665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-01-01DOI: 10.1504/ijcbdd.2020.10033060
Nikita Chordia, Deepak Bhayal, Priyesh Hardia
{"title":"In silico drug target identification and pharmacophore mapping for Leishmania donovani based on metabolic pathways","authors":"Nikita Chordia, Deepak Bhayal, Priyesh Hardia","doi":"10.1504/ijcbdd.2020.10033060","DOIUrl":"https://doi.org/10.1504/ijcbdd.2020.10033060","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"129 1","pages":"378-389"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86594798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-01-01DOI: 10.1504/ijcbdd.2020.10033059
Sana Ashiq, K. Ashiq
{"title":"In-silico analysis of PON1, PON2 and PON3 genes role in coronary artery disease","authors":"Sana Ashiq, K. Ashiq","doi":"10.1504/ijcbdd.2020.10033059","DOIUrl":"https://doi.org/10.1504/ijcbdd.2020.10033059","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"16 1","pages":"415-423"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85939861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-01-01DOI: 10.1504/IJCBDD.2020.113836
C. D. Vandana, K. Shanti, P. Karunakar, V. Chandramohan
The current study is aimed at substantiating the anticancer activity of phytocompounds identified from extracts of in vivo and in vitro propagated Justicia wynaadensis (Nees) T. Anderson using in silico molecular docking and dynamics study. Few phytocompounds with anticancer activity based on literature were selected from GC-MS results of aqueous extract, methanolic extract of callus and in vitro propagated leaf of Justicia wynaadensis respectively. Totally twelve ligands were docked with Thymidylate synthase, where the binding affinity and efficiencies were analysed and compared with the reference drug Capecitabine. The docking result suggested the presence of compounds with anticancer activity. All the twelve ligands showed binding affinity ranging from -5.0 kcal/mol to -8.4 kcal/mol. To investigate the mechanism of action of Campesterol, Stigmasterol and Capecitabine with the target protein, these compounds were subjected to dynamic simulation which revealed that Campesterol was more stable than Stigmasterol and could be a potential lead-like molecule.
本研究旨在利用硅分子对接和动力学研究的方法，证实从体内和体外繁殖的刺蒺藜(Justicia wynaadensis, Nees) T. Anderson)提取物中鉴定的植物化合物的抗癌活性。在文献分析的基础上，分别从白桦愈伤组织水提物、甲醇提物和离体繁殖叶的GC-MS结果中筛选出少量具有抗癌活性的植物化合物。共将12个配体与胸苷酸合成酶对接，分析其结合亲和力和效率，并与参比药物卡培他滨进行比较。对接结果提示存在具有抗癌活性的化合物。12种配体的结合亲合力在-5.0 ~ -8.4 kcal/mol之间。为了研究油菜甾醇、豆甾醇和卡培他滨与靶蛋白的作用机制，对这些化合物进行了动态模拟，结果表明油菜甾醇比豆甾醇更稳定，可能是潜在的类铅分子。
{"title":"In silico studies of bioactive phytocompounds with anticancer activity from in vivo and in vitro extracts of Justicia wynaadensis (Nees) T. Anderson","authors":"C. D. Vandana, K. Shanti, P. Karunakar, V. Chandramohan","doi":"10.1504/IJCBDD.2020.113836","DOIUrl":"https://doi.org/10.1504/IJCBDD.2020.113836","url":null,"abstract":"The current study is aimed at substantiating the anticancer activity of phytocompounds identified from extracts of in vivo and in vitro propagated Justicia wynaadensis (Nees) T. Anderson using in silico molecular docking and dynamics study. Few phytocompounds with anticancer activity based on literature were selected from GC-MS results of aqueous extract, methanolic extract of callus and in vitro propagated leaf of Justicia wynaadensis respectively. Totally twelve ligands were docked with Thymidylate synthase, where the binding affinity and efficiencies were analysed and compared with the reference drug Capecitabine. The docking result suggested the presence of compounds with anticancer activity. All the twelve ligands showed binding affinity ranging from -5.0 kcal/mol to -8.4 kcal/mol. To investigate the mechanism of action of Campesterol, Stigmasterol and Capecitabine with the target protein, these compounds were subjected to dynamic simulation which revealed that Campesterol was more stable than Stigmasterol and could be a potential lead-like molecule.","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"60 1","pages":"582-601"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89388973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-01-01DOI: 10.1504/ijcbdd.2020.107315
T. Samaha
{"title":"Interactions of Leptospiral PI-PLC with the membrane phosphoinositides: an insight of the protein-phospholipid association in the pathogenesis","authors":"T. Samaha","doi":"10.1504/ijcbdd.2020.107315","DOIUrl":"https://doi.org/10.1504/ijcbdd.2020.107315","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"49 1","pages":"200-208"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90588258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-01-01DOI: 10.1504/IJCBDD.2020.113823
S. Srinivasan, Y. Paat, Philmore Halls, Ruth Kalule, Thomas E. Harvey
{"title":"Predicting re-admission to hospital for diabetes treatment: a machine learning solution","authors":"S. Srinivasan, Y. Paat, Philmore Halls, Ruth Kalule, Thomas E. Harvey","doi":"10.1504/IJCBDD.2020.113823","DOIUrl":"https://doi.org/10.1504/IJCBDD.2020.113823","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"13 1","pages":"539-554"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81603066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-01-01DOI: 10.1504/IJCBDD.2020.113820
Achal Awasthi, Shenglong Tan, Travis S. Johnson, X. Mo, Kunjie Fan, Yan Zhang
{"title":"PgenePapers: a novel database and search tools of reported regulatory pseudogenes","authors":"Achal Awasthi, Shenglong Tan, Travis S. Johnson, X. Mo, Kunjie Fan, Yan Zhang","doi":"10.1504/IJCBDD.2020.113820","DOIUrl":"https://doi.org/10.1504/IJCBDD.2020.113820","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"37 1","pages":"504-519"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76457231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-01-01DOI: 10.1504/IJCBDD.2020.113822
M. Zucker, K. Coombes
{"title":"Generating simulated SNP array and sequencing data to assess genomic segmentation algorithms","authors":"M. Zucker, K. Coombes","doi":"10.1504/IJCBDD.2020.113822","DOIUrl":"https://doi.org/10.1504/IJCBDD.2020.113822","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"22 1","pages":"438-453"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76199602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-01-01DOI: 10.1504/IJCBDD.2020.113872
Bjarne R. Bartlett, Yong Zhu, Mark Menor, V. Khadka, Jicai Zhang, Jie Zheng, B. Jiang, Youping Deng
{"title":"Development of a RNA-Seq based prognostic signature for colon cancer","authors":"Bjarne R. Bartlett, Yong Zhu, Mark Menor, V. Khadka, Jicai Zhang, Jie Zheng, B. Jiang, Youping Deng","doi":"10.1504/IJCBDD.2020.113872","DOIUrl":"https://doi.org/10.1504/IJCBDD.2020.113872","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"95 1","pages":"488-503"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80654683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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