A sequence homology and bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2

A Grifoni, J Sidney, Y Zhang, RH Scheuermann… - Cell host & …, 2020 - cell.com
membrane protein, and nucleoproteins are shown in Figure 2. In the case of the spike
glycoprotein (Figure 2A), we identify … regions associated with high immune response rates. Three …

Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes

A Poran, D Harjanto, M Malloy, CM Arieta… - Genome medicine, 2020 - Springer
bioinformatics platform, we identify multiple putative epitopes that are potential targets for CD4
+ and CD8 + T cells… structural proteins are the spike protein (S), the membrane protein (M)…

The surfaceome of multiple myeloma cells suggests potential immunotherapeutic strategies and protein markers of drug resistance

ID Ferguson, B Patiño-Escobar, ST Tuomivaara… - Nature …, 2022 - nature.com
surface antigens and identify CCR10 as a promising target in … Human Protein Atlas 26 , as
well as bioinformatic prediction … ) was by far the most increased surface protein in CfzR cells, …

Identification of vaccine targets in pathogens and design of a vaccine using computational approaches

K Rawal, R Sinha, BA Abbasi, A Chaudhary, SK Nath… - Scientific reports, 2021 - nature.com
… screening, we filtered TC-CLB proteins using a set of bioinformatics tools. First, we used the
… family such as trans-sialidases, and mucin-associated surface protein were present in the …

Gene function and cell surface protein association analysis based on single-cell multiomics data

H Hu, Z Feng, H Lin, J Cheng, J Lyu, Y Zhang… - Computers in Biology …, 2023 - Elsevier
cell surface proteins have been the targets of the approved drugs for human diseases [22,28].
Cell surface proteinsmost studies and their potential functions have not been investigated. …

Cell surface thermal proteome profiling tracks perturbations and drug targets on the plasma membrane

M Kalxdorf, I Günthner, I Becher, N Kurzawa… - … Methods, 2021 - nature.com
… ) for quantified cell surface proteins in K562 cells by TPP without and with cell surface protein
… enrichment step on thermal stability measurements of cell surface proteins, we compared …

Proteomic dissection of large extracellular vesicle surfaceome unravels interactive surface platform

A Rai, H Fang, B Claridge, RJ Simpson… - Journal of …, 2021 - Wiley Online Library
… and therapeutic targets. However, our understanding of … The focus of this paper is directed
at defining surface proteinProteins selected for downstream bioinformatics analysis …

Design of protein-binding proteins from the target structure alone

L Cao, B Coventry, I Goreshnik, B Huang, W Sheffler… - Nature, 2022 - nature.com
most promising binding modes. We demonstrate the broad applicability of this approach
through the de novo design of binding proteins … For each of these surface proteins, we selected …

A human IgSF cell-surface interactome reveals a complex network of protein-protein interactions

WM Wojtowicz, J Vielmetter, RA Fernandes, DH Siepe… - Cell, 2020 - cell.com
cell-surface proteins (excluding antibodies and T cell receptors), along with other select proteins
… The IgSF is the largest and most functionally diverse family in the cell-surface proteome. …

Bioinformatics analysis of epitope-based vaccine design against the novel SARS-CoV-2

HZ Chen, LL Tang, XL Yu, J Zhou, YF Chang… - Infectious diseases of …, 2020 - Springer
… This study aimed to predict the protective epitopes with bioinformatics methods and resources
… The purpose of this study is to predict B-cell epitopes on spike protein and T-cell epitopes …