Journal of chemical theory and computation
Feb 23, 2024
Time-lagged independent component analysis (tICA) and the Markov state model (MSM) have been extensively employed for extracting conformational dynamics and kinetic community networks from unbiased trajectory ensembles. However, these techniques may ...
We introduce a computational approach for the design of target-specific peptides. Our method integrates a Gated Recurrent Unit-based Variational Autoencoder with Rosetta FlexPepDock for peptide sequence generation and binding affinity assessment. Sub...
Fluorescence correlation spectroscopy (FCS) techniques are well-established tools to investigate molecular dynamics in confocal and super-resolution microscopy. In practice, users often need to handle a variety of sample- or hardware-related artifact...
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic solvation ...
Journal of biomolecular structure & dynamics
Feb 12, 2024
Psoriasis brings economic and mental burdens to patients, the exact etiology and pathogenesis of psoriasis are still unclear. Compounds of herbal medicine have the potential for psoriasis treatment. This study aims to explore the characteristic genes...
International journal of biological macromolecules
Feb 8, 2024
The prevalence of metabolic diseases is increasing at a frightening rate year by year. The burgeoning development of deep learning enables drug design to be more efficient, selective, and structurally novel. The critical relevance of Histone deacetyl...
Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make...
Journal of biomolecular structure & dynamics
Jan 12, 2024
Recently, there has been significant attention on machine learning algorithms for predictive modeling. Prediction models for enzyme inhibitors are limited, and it is essential to account for chemical biases while developing them. The lack of repeatab...
Journal of chemical theory and computation
Jan 12, 2024
Protein thermodynamics is intimately tied to biological function and can enable processes such as signal transduction, enzyme catalysis, and molecular recognition. The relative free energies of conformations that contribute to these functional equili...
Journal of chemical theory and computation
Jan 11, 2024
With the ongoing development of peptide self-assembling materials, there is growing interest in exploring novel functional peptide sequences. From short peptides to long polypeptides, as the functionality increases, the sequence space is also expandi...