The State-of-the-art overview to application of deep learning in accurate protein design and structure prediction

S Saharkhiz, M Mostafavi, A Birashk, S Karimian… - Topics in Current …, 2024 - Springer
In recent years, there has been a notable increase in the scientific community's interest in
rational protein design. The prospect of designing an amino acid sequence that can reliably …

The power of molecular dynamics simulations and their applications to discover cysteine protease inhibitors

IJ dos Santos Nascimento… - Mini Reviews in …, 2024 - benthamdirect.com
A large family of enzymes with the function of hydrolyzing peptide bonds, called peptidases
or cysteine proteases (CPs), are divided into three categories according to the peptide chain …

MDSuite: comprehensive post-processing tool for particle simulations

S Tovey, F Zills, F Torres-Herrador, C Lohrmann… - Journal of …, 2023 - Springer
Abstract Particle-Based (PB) simulations, including Molecular Dynamics (MD), provide
access to system observables that are not easily available experimentally. However, in most …

Intrinsically Disordered Malaria Antigens: An Overview of Structures, Dynamics and Molecular Simulation Opportunities

PCC Silva, L Martínez - Journal of the Brazilian Chemical Society, 2024 - SciELO Brasil
The proteome of Plasmodium falciparum (Pf) is abundant in intrinsically disordered proteins
(IDPs). Their important roles in the malaria life cycle and the limitations of experimental and …

A polymeric nanocarrier that eradicates breast cancer stem cells and delivers chemotherapeutic drugs

L Lv, Y Shi, Z Deng, J Xu, Z Ye, J He, G Chen, X Yu… - Biomaterials …, 2023 - Springer
Background Drug nanocarriers can markedly reduce the toxicities and side effects of
encapsulated chemotherapeutic drugs in the clinic. However, these drug nanocarriers have …

Design, synthesis, biological evaluation and molecular docking studies of quinoline-anthranilic acid hybrids as potent anti-inflammatory drugs

S Siddique, K Hussain, N Shehzadi… - Organic & …, 2024 - pubs.rsc.org
Despite the high global prevalence, rheumatoid arthritis lacks a satisfactory treatment.
Hence, the present study is undertaken to design and synthesize novel anti-inflammatory …

Automatic molecular fragmentation by evolutionary optimisation

FCY Yu, JLG Vallejo, GMJ Barca - Journal of Cheminformatics, 2024 - Springer
Molecular fragmentation is an effective suite of approaches to reduce the formal
computational complexity of quantum chemistry calculations while enhancing their …

Drug-target Binding Affinity Prediction Based on Three-branched Multiscale Convolutional Neural Networks

Y Lu, J Liu, T Jiang, Z Cui, H Wu - Current Bioinformatics, 2023 - ingentaconnect.com
Background: New drugs are costly, time-consuming, and often accompanied by safety
concerns. With the development of deep learning, computer-aided drug design has become …

[HTML][HTML] LSTM-SAGDTA: Predicting Drug-target Binding Affinity with an Attention Graph Neural Network and LSTM Approach

W Qiu, Q Liang, L Yu, X Xiao, W Qiu… - Current Pharmaceutical …, 2024 - ncbi.nlm.nih.gov
Methods: Drug development is a vital research area that necessitates innovation and
collaboration to achieve significant breakthroughs. Computer-aided drug design provides a …

Unraveling the therapeutic potential of Senna singueana phytochemicals to attenuate pancreatic cancer using protein–protein interactions, molecular docking, and …

A Balkrishna, D Sharma, M Thapliyal, V Arya… - In Silico …, 2023 - Springer
Pancreatic cancer (PC) presents challenges due to limited treatment options and patients
seek complementary therapies alongside conventional treatments to improve well-being …