Computational approaches for organic semiconductors: from chemical and physical understanding to predicting new materials
While a complete understanding of organic semiconductor (OSC) design principles remains
elusive, computational methods─ ranging from techniques based in classical and quantum …
elusive, computational methods─ ranging from techniques based in classical and quantum …
Exploring and learning the universe of protein allostery using artificial intelligence augmented biophysical and computational approaches
Allosteric mechanisms are commonly employed regulatory tools used by proteins to
orchestrate complex biochemical processes and control communications in cells. The …
orchestrate complex biochemical processes and control communications in cells. The …
Accelerating cryptic pocket discovery using AlphaFold
Cryptic pockets, or pockets absent in ligand-free, experimentally determined structures, hold
great potential as drug targets. However, cryptic pocket openings are often beyond the reach …
great potential as drug targets. However, cryptic pocket openings are often beyond the reach …
An efficient path classification algorithm based on variational autoencoder to identify metastable path channels for complex conformational changes
Conformational changes (ie, dynamic transitions between pairs of conformational states)
play important roles in many chemical and biological processes. Constructing the Markov …
play important roles in many chemical and biological processes. Constructing the Markov …
Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations
The ability to predict and understand complex molecular motions occurring over diverse
timescales ranging from picoseconds to seconds and even hours in biological systems …
timescales ranging from picoseconds to seconds and even hours in biological systems …
The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition
Transporters are targeted by endogenous metabolites and exogenous molecules to reach
cellular destinations, but it is generally not understood how different substrate classes …
cellular destinations, but it is generally not understood how different substrate classes …
GraphVAMPnets for uncovering slow collective variables of self-assembly dynamics
Uncovering slow collective variables (CVs) of self-assembly dynamics is important to
elucidate its numerous kinetic assembly pathways and drive the design of novel structures …
elucidate its numerous kinetic assembly pathways and drive the design of novel structures …
[HTML][HTML] Protein representations: Encoding biological information for machine learning in biocatalysis
D Harding-Larsen, J Funk, NG Madsen… - Biotechnology …, 2024 - Elsevier
Enzymes offer a more environmentally friendly and low-impact solution to conventional
chemistry, but they often require additional engineering for their application in industrial …
chemistry, but they often require additional engineering for their application in industrial …
Memory unlocks the future of biomolecular dynamics: Transformative tools to uncover physical insights accurately and efficiently
Conformational changes underpin function and encode complex biomolecular mechanisms.
Gaining atomic-level detail of how such changes occur has the potential to reveal these …
Gaining atomic-level detail of how such changes occur has the potential to reveal these …
Toward a benchmark for Markov state models: The folding of HP35
Adopting a 300 μs long MD trajectory of the folding of villin headpiece (HP35) by DE Shaw
Research, we recently constructed a Markov state model (MSM) based on inter-residue …
Research, we recently constructed a Markov state model (MSM) based on inter-residue …