Computational design of structured loops for new protein functions
The ability to engineer the precise geometries, fine-tuned energetics and subtle dynamics
that are characteristic of functional proteins is a major unsolved challenge in the field of …
that are characteristic of functional proteins is a major unsolved challenge in the field of …
CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm
Motivation Regions that connect secondary structure elements in a protein are known as
loops, whose slight change will produce dramatic effect on the entire topology. This study …
loops, whose slight change will produce dramatic effect on the entire topology. This study …
A de novo protein structure prediction by iterative partition sampling, topology adjustment and residue-level distance deviation optimization
Motivation With the great progress of deep learning-based inter-residue contact/distance
prediction, the discrete space formed by fragment assembly cannot satisfy the distance …
prediction, the discrete space formed by fragment assembly cannot satisfy the distance …
Protein predictive modeling and simulation of mutations of Presenilin-1 familial Alzheimer's disease on the orthosteric site
Alzheimer's disease pathology is characterized by β-amyloid plaques and neurofibrillary
tangles. Amyloid precursor protein is processed by β and γ secretase, resulting in the …
tangles. Amyloid precursor protein is processed by β and γ secretase, resulting in the …
Constraint guided beta-sheet refinement for protein structure prediction
Protein structure prediction (PSP) is a crucial issue in Bioinformatics. PSP has its important
use in many vital research areas that include drug discovery. One of the important …
use in many vital research areas that include drug discovery. One of the important …
A variable neighbourhood descent heuristic for conformational search using a quantum annealer
Discovering the low-energy conformations of a molecule is of great interest to computational
chemists, with applications in in silico materials design and drug discovery. In this paper, we …
chemists, with applications in in silico materials design and drug discovery. In this paper, we …
Multiscale modeling of unfolding and bond dissociation of rubredoxin metalloprotein
Mechanical properties of proteins that have a crucial effect on their operation. This study
used a molecular dynamics simulation package to investigate rubredoxin unfolding on the …
used a molecular dynamics simulation package to investigate rubredoxin unfolding on the …
Thyroid Hormone Receptor Agonistic and Antagonistic Activity of Newly Synthesized Dihydroxylated Polybrominated Diphenyl Ethers: An In Vitro and In Silico …
Dihydroxylated polybrominated diphenyl ethers (DiOH-PBDEs) could be the metabolites of
PBDEs of some organisms or the natural products of certain marine bacteria and algae. OH …
PBDEs of some organisms or the natural products of certain marine bacteria and algae. OH …
Design and Synthesis of Crosslinked Helix Dimers as Protein Tertiary Structure Mimics
Crosslinked helix dimers (CHDs) are synthetic tertiary helical structure motifs designed to
modulate interactions of proteins with binding partners. Helix dimers serve as mimics of …
modulate interactions of proteins with binding partners. Helix dimers serve as mimics of …
Distance-guided protein folding based on generalized descent direction
Advances in the prediction of the inter-residue distance for a protein sequence have
increased the accuracy to predict the correct folds of proteins with distance information …
increased the accuracy to predict the correct folds of proteins with distance information …