Molecular docking in organic, inorganic, and hybrid systems: a tutorial review

M Mohanty, PS Mohanty - Monatshefte für Chemie-Chemical Monthly, 2023 - Springer
Molecular docking simulation is a very popular and well-established computational
approach and has been extensively used to understand molecular interactions between a …

Protein structure prediction: conventional and deep learning perspectives

VA Jisna, PB Jayaraj - The protein journal, 2021 - Springer
Protein structure prediction is a way to bridge the sequence-structure gap, one of the main
challenges in computational biology and chemistry. Predicting any protein's accurate …

Independent se (3)-equivariant models for end-to-end rigid protein docking

OE Ganea, X Huang, C Bunne, Y Bian… - arxiv preprint arxiv …, 2021 - arxiv.org
Protein complex formation is a central problem in biology, being involved in most of the cell's
processes, and essential for applications, eg drug design or protein engineering. We tackle …

Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints

JG Greener, SM Kandathil, DT Jones - Nature communications, 2019 - nature.com
The inapplicability of amino acid covariation methods to small protein families has limited
their use for structural annotation of whole genomes. Recently, deep learning has shown …

Recent advances and challenges in protein structure prediction

CX Peng, F Liang, YH **a, KL Zhao… - Journal of Chemical …, 2023 - ACS Publications
Artificial intelligence has made significant advances in the field of protein structure prediction
in recent years. In particular, DeepMind's end-to-end model, AlphaFold2, has demonstrated …

Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13

J Hou, T Wu, R Cao, J Cheng - Proteins: Structure, Function …, 2019 - Wiley Online Library
Predicting residue‐residue distance relationships (eg, contacts) has become the key
direction to advance protein structure prediction since 2014 CASP11 experiment, while …

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Z Guo, J Liu, J Skolnick, J Cheng - Nature Communications, 2022 - nature.com
Residue-residue distance information is useful for predicting tertiary structures of protein
monomers or quaternary structures of protein complexes. Many deep learning methods …

Interdependence of a mechanosensitive anion channel and glutamate receptors in distal wound signaling

J Moe-Lange, NM Gappel, M Machado, MM Wudick… - Science …, 2021 - science.org
Glutamate has dual roles in metabolism and signaling; thus, signaling functions must be
isolatable and distinct from metabolic fluctuations, as seen in low-glutamate domains at …

Recent progress of protein tertiary structure prediction

Q Wuyun, Y Chen, Y Shen, Y Cao, G Hu, W Cui, J Gao… - Molecules, 2024 - mdpi.com
The prediction of three-dimensional (3D) protein structure from amino acid sequences has
stood as a significant challenge in computational and structural bioinformatics for decades …

Protein design with deep learning

M Defresne, S Barbe, T Schiex - International Journal of Molecular …, 2021 - mdpi.com
Computational Protein Design (CPD) has produced impressive results for engineering new
proteins, resulting in a wide variety of applications. In the past few years, various efforts have …