Topic 07 -- Abstracts with Biological Entities (English) - 75 Topics / Sub-Topic Model 25 - 15 Topics

cite ad title authors publish year publish time dataset abstract mentions covid pmcid pubmed id doi cord uid topic weight Similarity scispacy Similarity specter
1 Pérez-Montoto_2009 Scoring function for DNA–drug docking of anticancer and antiparasitic compounds based on spectral moments of 2D lattice graphs for molecular dynamics trajectories Pérez-Montoto, Lázaro G.; Santana, Lourdes; González-Díaz, Humberto 2009 2009-11-30 PMC N PMC7127518 19604606.0 10.1016/j.ejmech.2009.06.011 58p5b2vw 0.836961 Saw_A_2019, Qi_Z_2018, Chang_2011, Zheng_2009, Liao_2006 González-Díaz_2009, Pérez-Montoto_2009
2 Liu_S_2012 Application of Consensus Scoring and Principal Component Analysis for Virtual Screening against β-Secretase (BACE-1) Liu, Shu; Fu, Rao; Zhou, Li-Hua; Chen, Sheng-Ping 2012 2012-06-11 COMM-USE N PMC3372491 22701601.0 10.1371/journal.pone.0038086 7vwpvcdd 0.821681 Saw_A_2019, Qi_Z_2018, Dai_Q_2012, Feng_2010
3 Xie_H_2014 3D QSAR Studies, Pharmacophore Modeling and Virtual Screening on a Series of Steroidal Aromatase Inhibitors Xie, Huiding; Qiu, Kaixiong; Xie, Xiaoguang 2014 2014-11-14 COMM-USE N PMC4264204 25405729.0 10.3390/ijms151120927 afx7hacm 0.804462 Saw_A_2019, Zhou_2011, Dai_Q_2012, Qi_Z_2018
4 Pereira_2015 QSAR-Assisted Virtual Screening of Lead-Like Molecules from Marine and Microbial Natural Sources for Antitumor and Antibiotic Drug Discovery Pereira, Florbela; Latino, Diogo A. R. S.; Gaudêncio, Susana P. 2015 2015-03-17 COMM-USE N PMC6272462 25789820.0 10.3390/molecules20034848 okp8ofl0 0.768177 Dai_Q_2012, Saw_A_2019, Qi_Z_2018, Chang_2011 Pereira_2014, Zhou_2010
5 Zhou_2010 QSAR models for predicting cathepsin B inhibition by small molecules—Continuous and binary QSAR models to classify cathepsin B inhibition activities of small molecules Zhou, Zhigang; Wang, Yanli; Bryant, Stephen H. 2010 2010-06-30 None N PMC2873115 20194042.0 10.1016/j.jmgm.2010.01.009 bs17igjs 0.732579 Saw_A_2019, Chang_2011, Qi_Z_2018, Dai_Q_2012, Feng_2010
6 Wang_2018 A Comprehensive In Silico Method to Study the QSTR of the Aconitine Alkaloids for Designing Novel Drugs Wang, Ming-Yang; Liang, Jing-Wei; Mohamed Olounfeh, Kamara; Sun, Qi; Zhao, Nan; Meng, Fan-Hao 2018 2018-09-18 COMM-USE N PMC6225272 30231506.0 10.3390/molecules23092385 fewy8y4a 0.709895 Qi_Z_2018, Saw_A_2019, Dai_Q_2012, Chang_2011
7 González-Díaz_2009 QSAR for RNases and theoretic–experimental study of molecular diversity on peptide mass fingerprints of a new Leishmania infantum protein González-Díaz, Humberto; Dea-Ayuela, María A.; Pérez-Montoto, Lázaro G.; Prado-Prado, Francisco J.; Agüero-Chapín, Guillermín; Bolas-Fernández, Francisco; Vazquez-Padrón, Roberto I.; Ubeira, Florencio M. 2009 2009-07-04 PMC N PMC7088557 19578942.0 10.1007/s11030-009-9178-0 vk8n8s2q 0.694425 Saw_A_2019, Qi_Z_2018, Chang_2011
8 Xu_J_2010 QSAR Studies on Andrographolide Derivatives as α-Glucosidase Inhibitors Xu, Jun; Huang, Sichao; Luo, Haibin; Li, Guoji; Bao, Jiaolin; Cai, Shaohui; Wang, Yuqiang 2010 2010-03-02 COMM-USE N PMC2869241 20479989.0 10.3390/ijms11030880 s0ps9rd0 0.680745 Qi_Z_2018, Saw_A_2019, Dai_Q_2012, Liao_2006, Feng_2010
9 Zhou_2011 Multi-conformation 3D QSAR study of benzenesulfonyl-pyrazol-ester compounds and their analogs as cathepsin B inhibitors Zhou, Zhigang; Wang, Yanli; Bryant, Stephen H. 2011 2011-09-01 PMC N PMC3167229 21798778.0 10.1016/j.jmgm.2011.06.013 kiwi87c9 0.673384 Saw_A_2019, Dai_Q_2012, Qi_Z_2018, Chang_2011
10 Pereira_2014 A Chemoinformatics Approach to the Discovery of Lead-Like Molecules from Marine and Microbial Sources En Route to Antitumor and Antibiotic Drugs Pereira, Florbela; Latino, Diogo A. R. S.; Gaudêncio, Susana P. 2014 2014-01-27 COMM-USE N PMC3944514 24473174.0 10.3390/md12020757 ud3x78u3 0.656333 Montgomery_2004, Sen_D_2018, Dai_Q_2012 Pereira_2015
11 Mei_H_2004 Identification of encoding proteins related to SARS-CoV Mei, Hu; Sun, Lili; Zhou, Yuan; Xiong, Qing; Li, Zhiliang 2004 2004-01-01 PMC N PMC7089014 10.1360/03wb0198 d8onhd04 0.644314
12 Durrant_2013 Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening Durrant, Jacob D.; Friedman, Aaron\nJ.; Rogers, Kathleen\nE.; McCammon, J. Andrew 2013 2013-06-04 PMC N PMC3735370 23734946.0 10.1021/ci400042y kauk7ze0 0.642955 Dai_Q_2012, Saw_A_2019, Qi_Z_2018 Li_H_2009
13 Pérez-Montoto_2009 Study of peptide fingerprints of parasite proteins and drug–DNA interactions with Markov-Mean-Energy invariants of biopolymer molecular-dynamic lattice networks Pérez-Montoto, Lázaro Guillermo; Dea-Ayuela, María Auxiliadora; Prado-Prado, Francisco J.; Bolas-Fernández, Francisco; Ubeira, Florencio M.; González-Díaz, Humberto 2009 2009-07-17 PMC N PMC7111648 10.1016/j.polymer.2009.05.055 zamrnne9 0.639384 Qi_Z_2018, Saw_A_2019, Chang_2011, Dai_Q_2012, Liao_2006
14 Roy_K_2015 Chapter 10 Other Related Techniques Roy, Kunal; Kar, Supratik; Das, Rudra Narayan 2015 2015-12-31 PMC N PMC7149793 10.1016/b978-0-12-801505-6.00010-7 a9q0tcgz 0.629084 Webb_2014, Sen_D_2018, Liou_2013 Ekins_2007, Zhang_2018
15 Kingsley_2016 Ranking Protein-Protein Docking Results using Steered Molecular Dynamics and Potential of Mean Force Calculations Kingsley, Laura J.; Esquivel-Rodríguez, Juan; Yang, Ying; Kihara, Daisuke; Lill, Markus A. 2016 2016-05-27 PMC N PMC5015890 27232548.0 10.1002/jcc.24412 04t18oqp 0.608428 Saw_A_2019, Qi_Z_2018, Chang_2011, Dai_Q_2012 Zhang_2018
16 Zhang_2018 Exploring the Binding Mechanism between Human Profilin (PFN1) and Polyproline-10 through Binding Mode Screening Leili Zhang; David R. Bell; Binquan Luan; Ruhong Zhou 2018 2018-09-16 BioRxiv N 10.1101/418830 40pe21lm 0.590025 Qi_Z_2018, Chang_2011, Saw_A_2019, Plewczyński_2008
17 Shao_2007 Structure‐Based Design and Synthesis of Highly Potent SARS‐CoV 3CL Protease Inhibitors Shao, Yi‐Ming; Yang, Wen‐Bin; Peng, Hung‐Pin; Hsu, Min‐Feng; Tsai, Keng‐Chang; Kuo, Tun‐Hsun; Wang, Andrew H.‐J.; Liang, Po‐Huang; Lin, Chun‐Hung; Yang, An‐Suei; Wong, Chi‐Huey 2007 2007-08-23 PMC N PMC7162026 17722121.0 10.1002/cbic.200700254 voem879q 0.580915 Qi_Z_2018
18 Li_H_2009 An effective docking strategy for virtual screening based on multi-objective optimization algorithm Li, Honglin; Zhang, Hailei; Zheng, Mingyue; Luo, Jie; Kang, Ling; Liu, Xiaofeng; Wang, Xicheng; Jiang, Hualiang 2009 2009-02-11 COMM-USE N PMC2753843 19210777.0 10.1186/1471-2105-10-58 udzz15bk 0.577000 Chang_2011, Qi_Z_2018, Saw_A_2019, Dai_Q_2012 Liu_S_2012
19 Webb_2014 Comparative Modeling of Drug Target Proteins☆ Webb, B.; Eswar, N.; Fan, H.; Khuri, N.; Pieper, U.; Dong, G.Q.; Sali, A. 2014 2014-12-31 PMC N PMC7157477 10.1016/b978-0-12-409547-2.11133-3 d66rz6dc 0.574834 Eswar_2007, Sen_D_2018 Eswar_2007
20 Eswar_2007 4.10 Comparative Modeling of Drug Target Proteins Eswar, N.; Sali, A. 2007 2007-12-31 PMC N PMC7151936 10.1016/b0-08-045044-x/00251-0 oqxh7egj 0.557085 Webb_2014, Qi_Z_2018 Webb_2014
21 Li_B_2008 Flow-injection chemiluminescence determination of chrysin and baicalein assisted by theoretical prediction of chemiluminescence behavior of chrysin and baicalein Li, Baoxin; Guo, Lili; Xu, Chunli; Ma, Limei 2008 2008-12-01 PMC N 10.1016/j.saa.2008.02.007 y5j07feh 0.542407 Qi_Z_2018, Chang_2011, Saw_A_2019, Mendizabal-Ruiz_2018
22 Zeng_2007 Mass spectral profiling: An effective tool for quality control of herbal medicines Zeng, Zhong-Da; Liang, Yi-Zeng; Chau, Foo-Tim; Chen, Shuo; Daniel, Mok Kam-Wah; Chan, Chi-On 2007 2007-12-05 PMC N PMC7119444 17996528.0 10.1016/j.aca.2007.09.057 fk8vz0g0 0.541901 Qi_Z_2018, Dai_Q_2012, Mendizabal-Ruiz_2018, Chang_2011
23 Jalali-Heravi_2009 Shuffling multivariate adaptive regression splines and adaptive neuro-fuzzy inference system as tools for QSAR study of SARS inhibitors Jalali-Heravi, M.; Asadollahi-Baboli, M.; Mani-Varnosfaderani, A. 2009 2009-12-05 PMC N PMC7126869 19665859.0 10.1016/j.jpba.2009.07.009 bf5rct4q 0.531819 Saw_A_2019, Liao_2006, Dai_Q_2012, Qi_Z_2018 Zhou_2010, Wang_2018
24 Kim_M_2013 A mass weighted chemical elastic network model elucidates closed form domain motions in proteins Kim, Min Hyeok; Seo, Sangjae; Jeong, Jay Il; Kim, Bum Joon; Liu, Wing Kam; Lim, Byeong Soo; Choi, Jae Boong; Kim, Moon Ki 2013 2013-03-18 PMC N PMC3649262 23456820.0 10.1002/pro.2244 p8n8va3y 0.518791 Qi_Z_2018, Kirillova_2009, Chang_2011, Liou_2013
25 Wąż_P_2013 Descriptors of 2D-dynamic graphs as a classification tool of DNA sequences Wąż, Piotr; Bielińska-Wąż, Dorota; Nandy, Ashesh 2013 2013-09-03 PMC N PMC7088265 10.1007/s10910-013-0249-1 x4z2iz7b 0.510448 Liao_2006, Dai_Q_2012, Chang_2011, Qi_Z_2018 Yu_J_2009, Zou_S_2014, Deng_2014, Qi_Z_2018
26 Li_Z_2007 Structural parameterization and functional prediction of antigenic polypeptome sequences with biological activity through quantitative sequence-activity models (QSAM) by molecular electronegativity edge-distance vector (VMED) Li, ZhiLiang; Wu, ShiRong; Chen, ZeCong; Ye, Nancy; Yang, ShengXi; Liao, ChunYang; Zhang, MengJun; Yang, Li; Mei, Hu; Yang, Yan; Zhao, Na; Zhou, Yuan; Zhou, Ping; Xiong, Qing; Xu, Hong; Liu, ShuShen; Ling, ZiHua; Chen, Gang; Li, GenRong 2007 2007-01-01 PMC N PMC7089106 17879071.0 10.1007/s11427-007-0080-7 7t4lizde 0.497618 Saw_A_2019, Qi_Z_2018, Chang_2011, Dai_Q_2012, Feng_2010
27 Fusani_2018 Active learning strategies with COMBINE analysis: new tricks for an old dog Fusani, Lucia; Cabrera, Alvaro Cortes 2018 2018-12-18 PMC N PMC7087723 30564994.0 10.1007/s10822-018-0181-3 oeokiay7 0.494967 Qi_Z_2018, Chang_2011, Saw_A_2019 Zhou_2010, Ekins_2007, Durrant_2013
28 Barlow_2012 In-silico studies in Chinese herbal medicines’ research: Evaluation of in-silico methodologies and phytochemical data sources, and a review of research to date Barlow, D.J.; Buriani, A.; Ehrman, T.; Bosisio, E.; Eberini, I.; Hylands, P.J. 2012 2012-04-10 PMC N PMC7126886 22326356.0 10.1016/j.jep.2012.01.041 udvrdglk 0.490041
29 Hou_Z_2016 Linear Quantitative Profiling Method Fast Monitors Alkaloids of Sophora Flavescens That Was Verified by Tri-Marker Analyses Hou, Zhifei; Sun, Guoxiang; Guo, Yong 2016 2016-08-16 COMM-USE N PMC4987015 27529425.0 10.1371/journal.pone.0161146 60udcsa7 0.486170 Chang_2011, Qi_Z_2018, Saw_A_2019, Dai_Q_2012, Feng_2010
30 Lin_X_2020 A Review on Applications of Computational Methods in Drug Screening and Design Lin, Xiaoqian; Li, Xiu; Lin, Xubo 2020 2020-03-18 COMM-USE N PMC7144386 32197324.0 10.3390/molecules25061375 xurmzmwj 0.476200 Ekins_2007
31 Du_Q_2017 2L-PCA: a two-level principal component analyzer for quantitative drug design and its applications Du, Qi-Shi; Wang, Shu-Qing; Xie, Neng-Zhong; Wang, Qing-Yan; Huang, Ri-Bo; Chou, Kuo-Chen 2017 2017-08-01 COMM-USE N PMC5642577 29050302.0 10.18632/oncotarget.19757 jbmj21c5 0.446318 Kirillova_2009, Liou_2013, Qi_Z_2018 Zhou_2010, Jia_J_2016, He_Z_2010, Wang_2018
32 Perez-Bello_2009 Alignment-free prediction of mycobacterial DNA promoters based on pseudo-folding lattice network or star-graph topological indices Perez-Bello, Alcides; Munteanu, Cristian Robert; Ubeira, Florencio M.; Lopes De Magalhães, Alexandre; Uriarte, Eugenio; González-Díaz, Humberto 2009 2009-02-07 PMC N PMC7126577 18992259.0 10.1016/j.jtbi.2008.09.035 us6ay892 0.438958 Qi_Z_2018, Chang_2011, Saw_A_2019, Dai_Q_2012
33 Chou_2011 Applications of analytical ultracentrifugation to protein size-and-shape distribution and structure-and-function analyses Chou, Chi-Yuan; Hsieh, Yi-Hui; Chang, Gu-Gang 2011 2011-05-31 PMC N PMC7128498 21087667.0 10.1016/j.ymeth.2010.11.002 cw2opick 0.408841 Qi_Z_2018, Dai_Q_2012, Chang_2011, Webb_2014
34 Nguyen_2019 GraphDTA: Predicting drug–target binding affinity with graph neural networks Thin Nguyen; Hang Le; Thomas P. Quinn; Thuc Le; Svetha Venkatesh 2019 2019-06-27 BioRxiv N 10.1101/684662 zult69f2 0.397468 Lee_C_2017
35 Khanna_2011 In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance Khanna, Varun; Ranganathan, Shoba 2011 2011-11-30 COMM-USE N PMC3278842 22373185.0 10.1186/1471-2105-12-s13-s25 ufdgi67q 0.397095 Lee_C_2017, Sen_D_2018, Chang_2011
36 Schuck_2009 On computational approaches for size-and-shape distributions from sedimentation velocity analytical ultracentrifugation Schuck, Peter 2009 2009-10-06 PMC N PMC2892069 19806353.0 10.1007/s00249-009-0545-7 ip0fxvhp 0.384261 Liou_2013, Qi_Z_2018, Mendizabal-Ruiz_2018 Chou_2011, Jonić_2016
37 Hu_L_2011 Predicting Biological Functions of Compounds Based on Chemical-Chemical Interactions Hu, Le-Le; Chen, Chen; Huang, Tao; Cai, Yu-Dong; Chou, Kuo-Chen 2011 2011-12-29 COMM-USE N PMC3248422 22220213.0 10.1371/journal.pone.0029491 0mn1gbll 0.380896 Qi_Z_2018, Chang_2011, Lee_C_2017, Saw_A_2019 Wang_2018
38 Ekins_2007 In silico pharmacology for drug discovery: applications to targets and beyond Ekins, S; Mestres, J; Testa, B 2007 2007-09-01 PMC N PMC1978280 17549046.0 10.1038/sj.bjp.0707306 qah877pk 0.379302 Sen_D_2018, Webb_2014 Wang_2018
39 Bakker_2018 Dynamic graphs, community detection, and Riemannian geometry Bakker, Craig; Halappanavar, Mahantesh; Visweswara Sathanur, Arun 2018 2018-03-29 COMM-USE N PMC6214282 30839776.0 10.1007/s41109-018-0059-2 ear9cyri 0.343438 Qi_Z_2018, Liou_2013 Coelho_2008