AIMC Topic: Protein Multimerization
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Dynamic Electronic Structure Fluctuations in the De Novo Peptide ACC-Dimer Revealed by First-Principles Theory and Machine Learning.
Journal of chemical information and modeling
Feb 14, 2025
Recent studies have reported long-range charge transport in peptide- and protein-based fibers and wires, rendering this class of materials as promising charge-conducting interfaces between biological systems and electronic devices. In the complex mol...
A synthetic protein-level neural network in mammalian cells.
Science (New York, N.Y.)
Dec 12, 2024
Artificial neural networks provide a powerful paradigm for nonbiological information processing. To understand whether similar principles could enable computation within living cells, we combined de novo-designed protein heterodimers and engineered v...
Binding and sensing diverse small molecules using shape-complementary pseudocycles.
Science (New York, N.Y.)
Jul 18, 2024
We describe an approach for designing high-affinity small molecule-binding proteins poised for downstream sensing. We use deep learning-generated pseudocycles with repeating structural units surrounding central binding pockets with widely varying sha...
Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane.
Journal of chemical theory and computation
Jun 25, 2024
The accurate calculation of equilibrium constants for protein-protein association is of fundamental importance to quantitative biology and remains an outstanding challenge for computational biophysics. Traditionally, equilibrium constants have been c...
EGG: Accuracy Estimation of Individual Multimeric Protein Models Using Deep Energy-Based Models and Graph Neural Networks.
International journal of molecular sciences
Jun 6, 2024
Reliable and accurate methods of estimating the accuracy of predicted protein models are vital to understanding their respective utility. Discerning how the quaternary structure conforms can significantly improve our collective understanding of cell ...
Interface design of SARS-CoV-2 symmetrical nsp7 dimer and machine learning-guided nsp7 sequence prediction reveals physicochemical properties and hotspots for nsp7 stability, adaptation, and therapeutic design.
Physical chemistry chemical physics : PCCP
May 8, 2024
The COVID-19 pandemic, driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), necessitates a profound understanding of the virus and its lifecycle. As an RNA virus with high mutation rates, SARS-CoV-2 exhibits genetic variability lea...
DeepSub: Utilizing Deep Learning for Predicting the Number of Subunits in Homo-Oligomeric Protein Complexes.
International journal of molecular sciences
Apr 28, 2024
The molecular weight (MW) of an enzyme is a critical parameter in enzyme-constrained models (ecModels). It is determined by two factors: the presence of subunits and the abundance of each subunit. Although the number of subunits (NS) can potentially ...
Inactive-enriched machine-learning models exploiting patent data improve structure-based virtual screening for PDL1 dimerizers.
Journal of advanced research
Jan 26, 2024
INTRODUCTION: Small-molecule Programmable Cell Death Protein 1/Programmable Death-Ligand 1 (PD1/PDL1) inhibition via PDL1 dimerization has the potential to lead to inexpensive drugs with better cancer patient outcomes and milder side effects. However...
Bound ion effects: Using machine learning method to study the kinesin Ncd's binding with microtubule.
Biophysical journal
Dec 30, 2023
Drosophila Ncd proteins are motor proteins that play important roles in spindle organization. Ncd and the tubulin dimer are highly charged. Thus, it is crucial to investigate Ncd-tubulin dimer interactions in the presence of ions, especially ions tha...
Integrating deep learning with microfluidics for biophysical classification of sickle red blood cells adhered to laminin.
PLoS computational biology
Nov 29, 2021
Sickle cell disease, a genetic disorder affecting a sizeable global demographic, manifests in sickle red blood cells (sRBCs) with altered shape and biomechanics. sRBCs show heightened adhesive interactions with inflamed endothelium, triggering painfu...
Erythrocytes, Abnormal
Erythrocyte Deformability
Computational Biology
Hemoglobin, Sickle
Microfluidics
Humans
Diagnosis, Computer-Assisted
Lab-On-A-Chip Devices
Anemia, Sickle Cell
Neural Networks, Computer
Deep Learning
Laminin
High-Throughput Screening Assays
In Vitro Techniques
Protein Multimerization
Image Interpretation, Computer-Assisted
Biophysical Phenomena
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