Literature DB >> 33993461

TUPDB: Target-Unrelated Peptide Data Bank.

Bifang He1,2, Shanshan Yang3, Jinjin Long3, Xue Chen3, Qianyue Zhang3, Hui Gao4, Heng Chen5, Jian Huang6.   

Abstract

The isolation of target-unrelated peptides (TUPs) through biopanning remains as a major problem of phage display selection experiments. These TUPs do not have any actual affinity toward targets of interest, which tend to be mistakenly identified as target-binding peptides. Therefore, an information portal for storing TUP data is urgently needed. Here, we present a TUP data bank (TUPDB), which is a comprehensive, manually curated database of approximately 73 experimentally verified TUPs and 1963 potential TUPs collected from TUPScan, the BDB database, and public research articles. The TUPScan tool has been integrated in TUPDB to facilitate TUP analysis. We believe that TUPDB can help identify and remove TUPs in future reports in the biopanning community. The database is of great importance to improving the quality of phage display-based epitope mapping and promoting the development of vaccines, diagnostics, and therapeutics. The TUPDB database is available at http://i.uestc.edu.cn/tupdb .

Keywords:  Biopanning; Database; Phage display; TUPDB; Target-unrelated peptides (TUPs)

Year:  2021        PMID: 33993461     DOI: 10.1007/s12539-021-00436-5

Source DB:  PubMed          Journal:  Interdiscip Sci        ISSN: 1867-1462            Impact factor:   2.233


  21 in total

1.  A target-unrelated peptide in an M13 phage display library traced to an advantageous mutation in the gene II ribosome-binding site.

Authors:  Leighanne A Brammer; Benjamin Bolduc; Jessica L Kass; Kristin M Felice; Christopher J Noren; Marilena Fitzsimons Hall
Journal:  Anal Biochem       Date:  2007-10-14       Impact factor: 3.365

Review 2.  Biased selection of propagation-related TUPs from phage display peptide libraries.

Authors:  Hesam Motaleb Zade; Reihaneh Keshavarz; Hosna Sadat Zahed Shekarabi; Babak Bakhshinejad
Journal:  Amino Acids       Date:  2017-06-29       Impact factor: 3.520

3.  Development and Application of Computational Methods in Phage Display Technology.

Authors:  Bifang He; Anthony Mackitz Dzisoo; Ratmir Derda; Jian Huang
Journal:  Curr Med Chem       Date:  2019       Impact factor: 4.530

Review 4.  Mimotope-based prediction of B-cell epitopes.

Authors:  Jian Huang; Bifang He; Peng Zhou
Journal:  Methods Mol Biol       Date:  2014

5.  Identification and characterization of mutant clones with enhanced propagation rates from phage-displayed peptide libraries.

Authors:  Kieu T H Nguyen; Marta A Adamkiewicz; Lauren E Hebert; Emily M Zygiel; Holly R Boyle; Christina M Martone; Carola B Meléndez-Ríos; Karen A Noren; Christopher J Noren; Marilena Fitzsimons Hall
Journal:  Anal Biochem       Date:  2014-06-19       Impact factor: 3.365

Review 6.  Phage display biopanning and isolation of target-unrelated peptides: in search of nonspecific binders hidden in a combinatorial library.

Authors:  Babak Bakhshinejad; Hesam Motaleb Zade; Hosna Sadat Zahed Shekarabi; Sara Neman
Journal:  Amino Acids       Date:  2016-09-20       Impact factor: 3.520

Review 7.  Phage Display Technology in Biomaterials Engineering: Progress and Opportunities for Applications in Regenerative Medicine.

Authors:  Ivone M Martins; Rui L Reis; Helena S Azevedo
Journal:  ACS Chem Biol       Date:  2016-10-10       Impact factor: 5.100

8.  Corruption of phage display libraries by target-unrelated clones: diagnosis and countermeasures.

Authors:  William D Thomas; Miriam Golomb; George P Smith
Journal:  Anal Biochem       Date:  2010-08-06       Impact factor: 3.365

9.  A novel peptide specifically binding to VEGF receptor suppresses angiogenesis in vitro and in vivo.

Authors:  Yuan Zhang; Bifang He; Kun Liu; Lin Ning; Delun Luo; Kai Xu; Wenli Zhu; Zhigang Wu; Jian Huang; Xun Xu
Journal:  Signal Transduct Target Ther       Date:  2017-05-12

10.  Epitope mapping of metuximab on CD147 using phage display and molecular docking.

Authors:  Bifang He; Canquan Mao; Beibei Ru; Hesong Han; Peng Zhou; Jian Huang
Journal:  Comput Math Methods Med       Date:  2013-06-03       Impact factor: 2.238

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  2 in total

1.  MPMABP: A CNN and Bi-LSTM-Based Method for Predicting Multi-Activities of Bioactive Peptides.

Authors:  You Li; Xueyong Li; Yuewu Liu; Yuhua Yao; Guohua Huang
Journal:  Pharmaceuticals (Basel)       Date:  2022-06-03

Review 2.  High-Throughput Monoclonal Antibody Discovery from Phage Libraries: Challenging the Current Preclinical Pipeline to Keep the Pace with the Increasing mAb Demand.

Authors:  Nicola Zambrano; Guendalina Froechlich; Dejan Lazarevic; Margherita Passariello; Alfredo Nicosia; Claudia De Lorenzo; Marco J Morelli; Emanuele Sasso
Journal:  Cancers (Basel)       Date:  2022-03-04       Impact factor: 6.639

  2 in total

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