Topic 11 -- 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 Zhang_2005 PRED(BALB/c): a system for the prediction of peptide binding to H2(d) molecules, a haplotype of the BALB/c mouse Zhang, Guang Lan; Srinivasan, Kellathur N.; Veeramani, Anitha; August, J. Thomas; Brusic, Vladimir 2005 2005-07-01 PMC N PMC1160239 15980450.0 10.1093/nar/gki479 y0wf456f 0.777179 Saw_A_2019, Qi_Z_2018, Chang_2011, Feng_2010, Lee_C_2017
2 Agrawal_2018 Prediction of Antimicrobial Potential of a Chemically Modified Peptide From Its Tertiary Structure Agrawal, Piyush; Raghava, Gajendra P. S. 2018 2018-10-26 COMM-USE N PMC6212470 30416494.0 10.3389/fmicb.2018.02551 4hlcxccy 0.773446 Qi_Z_2018, Saw_A_2019, Dai_Q_2012, Chang_2011, Lee_C_2017
3 Srinivasan_2004 Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens Srinivasan, K.N.; Zhang, G.L.; Khan, A.M.; August, J.T.; Brusic, V. 2004 2004-08-04 PMC N PMC7110022 15262812.0 10.1093/bioinformatics/bth943 vmc0rrrk 0.757664
4 Negi_2009 Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences Negi, Surendra S; Braun, Werner 2009 2009-07-01 COMM-USE N PMC2808184 20140073.0 lal14r4s 0.704959 Chang_2011, Qi_Z_2018
5 Qureshi_2013 VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses Qureshi, Abid; Thakur, Nishant; Kumar, Manoj 2013 2013-12-11 COMM-USE N PMC3878835 24330765.0 10.1186/1479-5876-11-305 ap60vws9 0.698262 Saw_A_2019, Lee_C_2017, Chang_2011
6 Zhang_2008 Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes Zhang, Guang Lan; Khan, Asif M; Srinivasan, Kellathur N; Heiny, AT; Lee, KX; Kwoh, Chee Keong; August, J Thomas; Brusic, Vladimir 2008 2008-02-13 COMM-USE N PMC2259420 18315850.0 10.1186/1471-2105-9-s1-s19 f0ahybvs 0.689700 Chang_2011
7 Beltrán_Lissabet_2019 AntiVPP 1.0: A portable tool for prediction of antiviral peptides Beltrán Lissabet, Jorge Félix; Belén, Lisandra Herrera; Farias, Jorge G. 2019 2019-04-30 PMC N PMC7094449 30802694.0 10.1016/j.compbiomed.2019.02.011 k935v0z9 0.653569 Lee_C_2017, Chang_2011, Qi_Z_2018, Saw_A_2019
8 Mayrose_2007 Pepitope: epitope mapping from affinity-selected peptides Mayrose, Itay; Penn, Osnat; Erez, Elana; Rubinstein, Nimrod D.; Shlomi, Tomer; Freund, Natalia Tarnovitski; Bublil, Erez M.; Ruppin, Eytan; Sharan, Roded; Gershoni, Jonathan M.; Martz, Eric; Pupko, Tal 2007 2007-12-01 PMC N PMC7110138 17977889.0 10.1093/bioinformatics/btm493 7rs4jtfh 0.636050 Qi_Z_2018, Dai_Q_2012, Montgomery_2004, Chang_2011, Lee_C_2017
9 Soam_2010 Improved Prediction of MHC Class I Binders/Non-Binders Peptides Through Artificial Neural Network Using Variable Learning Rate: SARS Corona Virus, a Case Study Soam, Sudhir Singh; Bhasker, Bharat; Mishra, Bhartendu Nath 2010 2010-11-13 PMC N PMC7123181 21431562.0 10.1007/978-1-4419-7046-6_22 71njvx7l 0.632325 Lee_C_2017, Saw_A_2019, Chang_2011, Qi_Z_2018
10 Chen_2012 PepMapper: A Collaborative Web Tool for Mapping Epitopes from Affinity-Selected Peptides Chen, Wenhan; Guo, William W.; Huang, Yanxin; Ma, Zhiqiang 2012 2012-05-25 COMM-USE N PMC3360666 22701536.0 10.1371/journal.pone.0037869 t3zampk7 0.614924 Lee_C_2017, Chang_2011, Qi_Z_2018, Saw_A_2019 Mayrose_2007, Sun_P_2015
11 Huang_2010 SAROTUP: Scanner and Reporter of Target-Unrelated Peptides Huang, Jian; Ru, Beibei; Li, Shiyong; Lin, Hao; Guo, Feng-Biao 2010 2010-03-21 PMC N PMC2842971 20339521.0 10.1155/2010/101932 hi7z3nob 0.602839 Lee_C_2017, Chang_2011
12 Sun_P_2015 Conformational B-Cell Epitope Prediction Method Based on Antigen Preprocessing and Mimotopes Analysis Sun, Pingping; Ju, Haixu; Zhang, Baowen; Gu, Yu; Liu, Bo; Huang, Yanxin; Zhang, Huijie; Li, Yuxin 2015 2015-01-29 COMM-USE N PMC4326220 25705652.0 10.1155/2015/257030 qk1pr335 0.589863 Saw_A_2019, Chang_2011, Lee_C_2017, Dai_Q_2012, Qi_Z_2018
13 He_Y_2010 Vaxign: The First Web-Based Vaccine Design Program for Reverse Vaccinology and Applications for Vaccine Development He, Yongqun; Xiang, Zuoshuang; Mobley, Harry L. T. 2010 2010-07-04 PMC N PMC2910479 20671958.0 10.1155/2010/297505 wczw4vn1 0.582130 Chang_2011, Lee_C_2017
14 Zhang_2013 A combination of epitope prediction and molecular docking allows for good identification of MHC class I restricted T-cell epitopes Zhang, Xue Wu 2013 2013-08-31 PMC N PMC7106517 23666426.0 10.1016/j.compbiolchem.2013.03.003 9lqh0evn 0.580412
15 EL-Manzalawy_2008 Predicting linear B-cell epitopes using string kernels EL-Manzalawy, Yasser; Dobbs, Drena; Honavar, Vasant 2008 2008-07-01 None N PMC2683948 18496882.0 10.1002/jmr.893 rtpbltkf 0.564925 Saw_A_2019, Chang_2011, Qi_Z_2018, Lee_C_2017, Dai_Q_2012
16 Xu_Y_2015 Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine Xu, Yongtao; Yu, Shui; Zou, Jian-Wei; Hu, Guixiang; Rahman, Noorsaadah A. B. D.; Othman, Rozana Binti; Tao, Xia; Huang, Meilan 2015 2015-12-04 COMM-USE N PMC4670226 26636321.0 10.1371/journal.pone.0144171 v4xue7ha 0.547108
17 Qureshi_2015 AVP‐IC(50)Pred: Multiple machine learning techniques‐based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC(50)) Qureshi, Abid; Tandon, Himani; Kumar, Manoj 2015 2015-11-26 None N PMC7161829 26213387.0 10.1002/bip.22703 a6y0eoov 0.540292 Saw_A_2019, Lee_C_2017, Qi_Z_2018, Dai_Q_2012, Chang_2011
18 Liu_W_2006 Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models Liu, Wen; Meng, Xiangshan; Xu, Qiqi; Flower, Darren R; Li, Tongbin 2006 2006-03-31 COMM-USE N PMC1513606 16579851.0 10.1186/1471-2105-7-182 ltf82dh3 0.516329 Dai_Q_2012, Saw_A_2019, Chang_2011, Sen_D_2018, Qi_Z_2018 Soam_2010
19 Qiu_T_2018 CE-BLAST makes it possible to compute antigenic similarity for newly emerging pathogens Qiu, Tianyi; Yang, Yiyan; Qiu, Jingxuan; Huang, Yang; Xu, Tianlei; Xiao, Han; Wu, Dingfeng; Zhang, Qingchen; Zhou, Chen; Zhang, Xiaoyan; Tang, Kailin; Xu, Jianqing; Cao, Zhiwei 2018 2018-05-02 None N PMC5932059 29720583.0 10.1038/s41467-018-04171-2 2upc2spn 0.485626
20 van_Weezep_2019 PCR diagnostics: In silico validation by an automated tool using freely available software programs van Weezep, Erik; Kooi, Engbert A.; van Rijn, Piet A. 2019 2019-08-31 PMC N PMC7113775 31095975.0 10.1016/j.jviromet.2019.05.002 ajzk86rq 0.450862 Chang_2011, Lee_C_2017, Montgomery_2004
21 Sathiamurthy_2005 An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities Sathiamurthy, Muthuraman; Peters, Bjoern; Bui, Huynh-Hoa; Sidney, John; Mokili, John; Wilson, Stephen S; Fleri, Ward; McGuinness, Deborah L; Bourne, Philip E; Sette, Alessandro 2005 2005-09-20 COMM-USE N PMC1287064 16305755.0 10.1186/1745-7580-1-2 zwbc7nnn 0.432848
22 Huang_2006 MIMOX: a web tool for phage display based epitope mapping Huang, Jian; Gutteridge, Alex; Honda, Wataru; Kanehisa, Minoru 2006 2006-10-12 COMM-USE N PMC1618411 17038191.0 10.1186/1471-2105-7-451 1ypgij14 0.411368 Montgomery_2004, Lee_C_2017, Lu_Q_2006, Chang_2011, Qi_Z_2018 Mayrose_2007
23 Sollner_2008 Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins Sollner, Johannes; Grohmann, Rainer; Rapberger, Ronald; Perco, Paul; Lukas, Arno; Mayer, Bernd 2008 2008-01-07 COMM-USE N PMC2244602 18179690.0 10.1186/1745-7580-4-1 ml2luc1t 0.410577 Chang_2011, Qi_Z_2018, Lee_C_2017, Kirillova_2009
24 Qureshi_2016 AVCpred: an integrated web server for prediction and design of antiviral compounds Qureshi, Abid; Kaur, Gazaldeep; Kumar, Manoj 2016 2016-09-09 PMC N PMC7162012 27490990.0 10.1111/cbdd.12834 gsv6dh36 0.399146 Lee_C_2017, Chang_2011, Santillana_2014
25 Barbarini_2011 Prediction of Peptide Reactivity with Human IVIg through a Knowledge-Based Approach Barbarini, Nicola; Tiengo, Alessandra; Bellazzi, Riccardo 2011 2011-08-24 COMM-USE N PMC3160895 21887285.0 10.1371/journal.pone.0023616 9gozwdng 0.368784 Qi_Z_2018, Chang_2011, Saw_A_2019 Sollner_2008
26 González-Díaz_2014 Model for Vaccine Design by Prediction of B-Epitopes of IEDB Given Perturbations in Peptide Sequence, In Vivo Process, Experimental Techniques, and Source or Host Organisms González-Díaz, Humberto; Pérez-Montoto, Lázaro G.; Ubeira, Florencio M. 2014 2014-01-12 COMM-USE N PMC3987976 24741624.0 10.1155/2014/768515 uh5rkjwx 0.365122 Qi_Z_2018, Chang_2011, Saw_A_2019
27 Cao_Y_2005 Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates Cao, Youfang; Wang, Lianjie; Xu, Kexue; Kou, Chunhai; Zhang, Yulei; Wei, Guifang; He, Junjian; Wang, Yunfang; Zhao, Liping 2005 2005-07-26 COMM-USE N PMC1183192 16042814.0 10.1186/1471-2105-6-190 whoydkd5 0.311430 Chang_2011, Saw_A_2019, Dai_Q_2012, Saw_A_2019