Software for molecular docking: a review
Molecular docking methodology explores the behavior of small molecules in the binding site
of a target protein. As more protein structures are determined experimentally using X-ray …
of a target protein. As more protein structures are determined experimentally using X-ray …
Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
SARS-CoV-2 infection depends on cellular heparan sulfate and ACE2
TM Clausen, DR Sandoval, CB Spliid, J Pihl… - Cell, 2020 - cell.com
We show that SARS-CoV-2 spike protein interacts with both cellular heparan sulfate and
angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain (RBD) …
angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain (RBD) …
Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2
Abstract Angiotensin converting enzyme 2 (ACE2)(EC: 3.4. 17.23) is a transmembrane
protein which is considered as a receptor for spike protein binding of novel coronavirus …
protein which is considered as a receptor for spike protein binding of novel coronavirus …
SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to down-regulate MHC-I surface expression
N Arshad, M Laurent-Rolle… - Proceedings of the …, 2023 - National Acad Sciences
Major histocompatibility complex class I (MHC-I) molecules, which are dimers of a
glycosylated polymorphic transmembrane heavy chain and the small-protein β2 …
glycosylated polymorphic transmembrane heavy chain and the small-protein β2 …
The ClusPro web server for protein–protein docking
Abstract The ClusPro server (https://cluspro. org) is a widely used tool for protein–protein
docking. The server provides a simple home page for basic use, requiring only two files in …
docking. The server provides a simple home page for basic use, requiring only two files in …
New additions to the C lus P ro server motivated by CAPRI
The heavily used protein–protein docking server ClusPro performs three computational
steps as follows:(1) rigid body docking,(2) RMSD based clustering of the 1000 lowest energy …
steps as follows:(1) rigid body docking,(2) RMSD based clustering of the 1000 lowest energy …
Glycosaminoglycan-based hydrogels capture inflammatory chemokines and rescue defective wound healing in mice
N Lohmann, L Schirmer, P Atallah, E Wandel… - Science translational …, 2017 - science.org
Excessive production of inflammatory chemokines can cause chronic inflammation and thus
impair cutaneous wound healing. Capturing chemokine signals using wound dressing …
impair cutaneous wound healing. Capturing chemokine signals using wound dressing …
Exploring the out of sight antigens of SARS-CoV-2 to design a candidate multi-epitope vaccine by utilizing immunoinformatics approaches
SARS-CoV-2 causes a severe respiratory disease called COVID-19. Currently, global health
is facing its devastating outbreak. However, there is no vaccine available against this virus …
is facing its devastating outbreak. However, there is no vaccine available against this virus …
Performance and its limits in rigid body protein-protein docking
The development of fast Fourier transform (FFT) algorithms enabled the sampling of billions
of complex conformations and thus revolutionized protein-protein docking. FFT-based …
of complex conformations and thus revolutionized protein-protein docking. FFT-based …