Computational approaches to therapeutic antibody design: established methods and emerging trends
Antibodies are proteins that recognize the molecular surfaces of potentially noxious
molecules to mount an adaptive immune response or, in the case of autoimmune diseases …
molecules to mount an adaptive immune response or, in the case of autoimmune diseases …
Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
Molecular docking is a computational method for predicting the placement of ligands in the
binding sites of their receptor (s). In this review, we discuss the methodological …
binding sites of their receptor (s). In this review, we discuss the methodological …
The HDOCK server for integrated protein–protein docking
Abstract The HDOCK server (http://hdock. phys. hust. edu. cn/) is a highly integrated suite of
homology search, template-based modeling, structure prediction, macromolecular docking …
homology search, template-based modeling, structure prediction, macromolecular docking …
HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA
Protein–protein interactions (PPIs) play an important role in the different functions of cells,
but accurate prediction of the three-dimensional structures for PPIs is still a notoriously …
but accurate prediction of the three-dimensional structures for PPIs is still a notoriously …
Molecular docking as a popular tool in drug design, an in silico travel
New molecular modeling approaches, driven by rapidly improving computational platforms,
have allowed many success stories for the use of computer-assisted drug design in the …
have allowed many success stories for the use of computer-assisted drug design in the …
[HTML][HTML] Protein–peptide docking: opportunities and challenges
Highlights•We provide an overview of protein-peptide docking methods and their
applications.•Peptide docking tools can be divided on template-based, local and global …
applications.•Peptide docking tools can be divided on template-based, local and global …
Benchmarking of different molecular docking methods for protein-peptide docking
Background Molecular docking studies on protein-peptide interactions are a challenging
and time-consuming task because peptides are generally more flexible than proteins and …
and time-consuming task because peptides are generally more flexible than proteins and …
Identification of a potential peptide inhibitor of SARS-CoV-2 targeting its entry into the host cells
Background and objective Coronavirus disease (COVID-19) is an ongoing pandemic
caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Due to the …
caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Due to the …
Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?
Predicting the structure and thermodynamics of protein–protein interactions (PPIs) are key to
a proper understanding and modulation of their function. Since experimental methods might …
a proper understanding and modulation of their function. Since experimental methods might …
Search strategies and evaluation in protein–protein docking: principles, advances and challenges
SY Huang - Drug discovery today, 2014 - Elsevier
Highlights•Search strategies of current protein–protein docking algorithms were
reviewed.•Challenges and future directions of established approaches were discussed.•Post …
reviewed.•Challenges and future directions of established approaches were discussed.•Post …