Machine learning-guided protein engineering

P Kouba, P Kohout, F Haddadi, A Bushuiev… - ACS …, 2023 - ACS Publications
Recent progress in engineering highly promising biocatalysts has increasingly involved
machine learning methods. These methods leverage existing experimental and simulation …

In silico structural analysis exploring conformational folding of protein variants in Alzheimer's disease

E Efraimidis, MG Krokidis, TP Exarchos… - International Journal of …, 2023 - mdpi.com
Accurate protein structure prediction using computational methods remains a challenge in
molecular biology. Recent advances in AI-powered algorithms provide a transformative …

Global Survey of Protein Dynamic Properties

CC Konkankit, S Rackovsky - The Journal of Physical Chemistry B, 2023 - ACS Publications
Using tools developed to study the dynamic bioinformatics of proteins, we are able to study
the dynamic characteristics of very large numbers of protein sequences simultaneously. We …

Are Protein Shape-Encoded Lowest-Frequency Motions a Key Phenotype Selected by Evolution?

L Orellana - Applied Sciences, 2023 - mdpi.com
At the very deepest molecular level, the mechanisms of life depend on the operation of
proteins, the so-called “workhorses” of the cell. Proteins are nanoscale machines that …

New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions

K Jia, M Kilinc, RL Jernigan - Frontiers in Bioinformatics, 2023 - frontiersin.org
Understanding protein sequences and how they relate to the functions of proteins is
extremely important. One of the most basic operations in bioinformatics is sequence …

dwMLCS: An Efficient MLCS Algorithm Based on Dynamic and Weighted Directed Acyclic Graph

C Yu, D Gao, X Guo, H Ma, Y Zhao… - IEEE/ACM Transactions …, 2024 - ieeexplore.ieee.org
The problem of finding the longest common subsequence (MLCS) for multiple sequences is
a computationally intensive and challenging problem that has significant applications in …

Unveiling Conserved Allosteric Hot Spots in Protein Domains from Sequences

A Hacisuleyman, D Fasshauer - bioRxiv, 2024 - biorxiv.org
The amino acid sequence determines the structure, function, and dynamics of a protein. In
recent years, enormous progress has been made in translating sequence information into …

Deep Learning Methods for Protein Representation and Function Prediction: A Comprehensive Overview

Z Ren - papers.ssrn.com
Protein function prediction is a critical goal in bioinformatics, playing a central role in
understanding biological processes and advancing applications such as drug discovery and …