[HTML][HTML] Research on Bitter Peptides in the Field of Bioinformatics: A Comprehensive Review

S Liu, T Shi, J Yu, R Li, H Lin, K Deng - International Journal of Molecular …, 2024 - mdpi.com
Bitter peptides are small molecular peptides produced by the hydrolysis of proteins under
acidic, alkaline, or enzymatic conditions. These peptides can enhance food flavor and offer …

[HTML][HTML] Structure-based protein and small molecule generation using EGNN and diffusion models: A comprehensive review

F Soleymani, E Paquet, HL Viktor… - Computational and …, 2024 - Elsevier
Recent breakthroughs in deep learning have revolutionized protein sequence and structure
prediction. These advancements are built on decades of protein design efforts, and are …

Accelerating Diffusion Models with Parallel Sampling: Inference at Sub-Linear Time Complexity

H Chen, Y Ren, L Ying, GM Rotskoff - arXiv preprint arXiv:2405.15986, 2024 - arxiv.org
Diffusion models have become a leading method for generative modeling of both image and
scientific data. As these models are costly to train and evaluate, reducing the inference cost …

Leveraging Deep Generative Model For Computational Protein Design And Optimization

B Lai - arXiv preprint arXiv:2408.17241, 2024 - arxiv.org
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living
matter and have tremendous implications in healthcare, manufacturing, and biotechnology …

Multi-modal conditioning for metal-organic frameworks generation using 3D modeling techniques

J Park, Y Lee, J Kim - 2024 - chemrxiv.org
The design of porous materials with user-desired properties has been a great interest for the
last few decades. However, the flexibility of target properties has been highly limited, and …

Parallel Sampling of Protein-Ligand Dynamics

MR Masters, AH Mahmoud, MA Lill - bioRxiv, 2024 - biorxiv.org
Molecular dynamics (MD) simulations of protein-ligand complexes are essential for
computer-aided drug design. In particular they enable the calculation of free energies and …

An outlook on structural biology after A lpha F old: tools, limits and perspectives

S Rosignoli, M Pacelli, F Manganiello, A Paiardini - FEBS Open Bio - Wiley Online Library
AlphaFold and similar groundbreaking, AI‐based tools, have revolutionized the field of
structural bioinformatics, with their remarkable accuracy in ab‐initio protein structure …