[HTML][HTML] Homology modeling in the time of collective and artificial intelligence
Homology modeling is a method for building protein 3D structures using protein primary
sequence and utilizing prior knowledge gained from structural similarities with other …
sequence and utilizing prior knowledge gained from structural similarities with other …
Protein function analysis through machine learning
Machine learning (ML) has been an important arsenal in computational biology used to
elucidate protein function for decades. With the recent burgeoning of novel ML methods and …
elucidate protein function for decades. With the recent burgeoning of novel ML methods and …
DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function
Motivation Predicting protein structures with high accuracy is a critical challenge for the
broad community of life sciences and industry. Despite progress made by deep neural …
broad community of life sciences and industry. Despite progress made by deep neural …
Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?
J Kapla, I Rodríguez-Espigares, F Ballante… - PLoS Computational …, 2021 - journals.plos.org
The determination of G protein-coupled receptor (GPCR) structures at atomic resolution has
improved understanding of cellular signaling and will accelerate the development of new …
improved understanding of cellular signaling and will accelerate the development of new …
Driven to near‐experimental accuracy by refinement via molecular dynamics simulations
Protein model refinement has been an essential part of successful protein structure
prediction. Molecular dynamics simulation‐based refinement methods have shown …
prediction. Molecular dynamics simulation‐based refinement methods have shown …
Direct experimental observation of blue-light-induced conformational change and intermolecular interactions of cryptochrome
P Li, H Cheng, V Kumar, CS Lupala, X Li, Y Shi… - Communications …, 2022 - nature.com
Cryptochromes are blue light receptors that mediate circadian rhythm and magnetic sensing
in various organisms. A typical cryptochrome consists of a conserved photolyase homology …
in various organisms. A typical cryptochrome consists of a conserved photolyase homology …
Systematic exploration of protein conformational space using a distance geometry approach
The optimization approaches classically used during the determination of protein structure
encounter various difficulties, especially when the size of the conformational space is large …
encounter various difficulties, especially when the size of the conformational space is large …
Incorporating a multiobjective knowledge-based energy function into differential evolution for protein structure prediction
Despite the rapid development of computer techniques and the unremitting efforts of
researchers, the protein structure prediction (PSP) problem remains challenging in …
researchers, the protein structure prediction (PSP) problem remains challenging in …
Solvent Accessibility Promotes Rotamer Errors during Protein Modeling with Major Side-Chain Prediction Programs
Side-chain rotamer prediction is one of the most critical late stages in protein 3D structure
building. Highly advanced and specialized algorithms (eg, FASPR, RASP, SCWRL4, and …
building. Highly advanced and specialized algorithms (eg, FASPR, RASP, SCWRL4, and …
Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling
The most frequently used approach for protein structure prediction is currently homology
modeling. The 3D model building phase of this methodology is critical for obtaining an …
modeling. The 3D model building phase of this methodology is critical for obtaining an …