The trRosetta server for fast and accurate protein structure prediction
The trRosetta (transform-restrained Rosetta) server is a web-based platform for fast and
accurate protein structure prediction, powered by deep learning and Rosetta. With the input …
accurate protein structure prediction, powered by deep learning and Rosetta. With the input …
Pragmatic coarse-graining of proteins: models and applications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …
proteins with other molecules are often difficult to assess by experimental techniques …
Molecular docking in organic, inorganic, and hybrid systems: a tutorial review
M Mohanty, PS Mohanty - Monatshefte für Chemie-Chemical Monthly, 2023 - Springer
Molecular docking simulation is a very popular and well-established computational
approach and has been extensively used to understand molecular interactions between a …
approach and has been extensively used to understand molecular interactions between a …
Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA
Bacteriophage T7 gp4 helicase has served as a model system for understanding
mechanisms of hexameric replicative helicase translocation. The mechanistic basis of how …
mechanisms of hexameric replicative helicase translocation. The mechanistic basis of how …
GraphGPSM: a global scoring model for protein structure using graph neural networks
G He, J Liu, D Liu, G Zhang - Briefings in bioinformatics, 2023 - academic.oup.com
The scoring models used for protein structure modeling and ranking are mainly divided into
unified field and protein-specific scoring functions. Although protein structure prediction has …
unified field and protein-specific scoring functions. Although protein structure prediction has …
Exploring the interplay between disordered and ordered oligomer channels on the aggregation energy landscapes of α-synuclein
The abnormal aggregation of α-synulcein is associated with multiple neurodegenerative
diseases such as Parkinson's disease. The hydrophobic non-amyloid component (NAC) …
diseases such as Parkinson's disease. The hydrophobic non-amyloid component (NAC) …
Protein structure prediction in casp13 using awsem-suite
Recently several techniques have emerged that significantly enhance the quality of
predictions of protein tertiary structures. In this study, we describe the performance of …
predictions of protein tertiary structures. In this study, we describe the performance of …
Early-Stage Oligomerization of Prion-like Polypeptides Reveals the Molecular Mechanism of Amyloid-Disrupting Capacity by Proline Residues
TY Lin, YW Ma, MY Tsai - The Journal of Physical Chemistry B, 2023 - ACS Publications
Proline cis/trans isomerization governs protein local conformational changes via its local
mechanical rigidity. The amyloid-disrupting capacity of proline is widely acknowledged; …
mechanical rigidity. The amyloid-disrupting capacity of proline is widely acknowledged; …
Identification of Antimicrobial Peptides Isolated From the Skin Mucus of African Catfish, Clarias gariepinus (Burchell, 1822)
Antimicrobial peptides (AMPs) constitute a broad range of bioactive compounds in diverse
organisms, including fish. They are effector molecules for the innate immune response …
organisms, including fish. They are effector molecules for the innate immune response …
Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
In this paper we report the improvements and extensions of the UNRES server (https://unres-
server. chem. ug. edu. pl) for physics-based simulations with the coarse-grained UNRES …
server. chem. ug. edu. pl) for physics-based simulations with the coarse-grained UNRES …