Dickkopf-1: A promising target for cancer immunotherapy

HY Chu, Z Chen, L Wang, ZK Zhang, X Tan… - Frontiers in …, 2021 - frontiersin.org
Clinical studies in a range of cancers have detected elevated levels of the Wnt antagonist
Dickkopf-1 (DKK1) in the serum or tumors of patients, and this was frequently associated …

Advancements and hurdles in the development of a vaccine for triple-negative breast cancer: A comprehensive review of multi-omics and immunomics strategies

T Dhanushkumar, ME Santhosh, PK Selvam… - Life Sciences, 2024 - Elsevier
Abstract Triple-Negative Breast Cancer (TNBC) presents a significant challenge in oncology
due to its aggressive behavior and limited therapeutic options. This review explores the …

A self-consistent sonification method to translate amino acid sequences into musical compositions and application in protein design using artificial intelligence

CH Yu, Z Qin, FJ Martin-Martinez, MJ Buehler - ACS nano, 2019 - ACS Publications
We report a self-consistent method to translate amino acid sequences into audible sound,
use the representation in the musical space to train a neural network, and then apply it to …

iHyd-LysSite (EPSV): identifying hydroxylysine sites in protein using statistical formulation by extracting enhanced position and sequence variant feature technique

MK Mahmood, A Ehsan, YD Khan… - Current Genomics, 2020 - ingentaconnect.com
Introduction: Hydroxylation is one of the most important post-translational modifications
(PTM) in cellular functions and is linked to various diseases. The addition of one of the …

Sonification based de novo protein design using artificial intelligence, structure prediction, and analysis using molecular modeling

CH Yu, MJ Buehler - APL bioengineering, 2020 - pubs.aip.org
We report the use of a deep learning model to design de novo proteins, based on the
interplay of elementary building blocks via hierarchical patterns. The deep neural network …

[HTML][HTML] PCPD: Plant cytochrome P450 database and web-based tools for structural construction and ligand docking

H Wang, Q Wang, Y Liu, X Liao, H Chu… - Synthetic and systems …, 2021 - Elsevier
Plant cytochrome P450s play key roles in the diversification and functional modification of
plant natural products. Although over 200,000 plant P450 gene sequences have been …

Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2

A Dwivedy, R Mariadasse, M Ahmad… - PLoS Computational …, 2021 - journals.plos.org
Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA
polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of …

VHH Structural Modelling Approaches: A Critical Review

P Vishwakarma, AM Vattekatte, N Shinada… - International Journal of …, 2022 - mdpi.com
VHH, ie, VH domains of camelid single-chain antibodies, are very promising therapeutic
agents due to their significant physicochemical advantages compared to classical …

PDB-2-PBv3. 0: An updated protein block database

MP Karuppasamy, S Venkateswaran… - … of Bioinformatics and …, 2020 - World Scientific
Our protein block (PB) sequence database PDB-2-PBv1. 0 provides PB sequences and
dihedral angles for 74,297 protein structures comprising of 103,252 protein chains of Protein …

Artificial intelligence method to design and fold alpha-helical structural proteins from the primary amino acid sequence

Z Qin, L Wu, H Sun, S Huo, T Ma, E Lim… - Extreme Mechanics …, 2020 - Elsevier
The development of rational techniques to discover new mechanically relevant proteins for
use in variety of applications ranging from mechanics, agriculture to biotechnology remains …