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 …
Antibody structure and function: the basis for engineering therapeutics
ML Chiu, DR Goulet, A Teplyakov, GL Gilliland - Antibodies, 2019 - mdpi.com
Antibodies and antibody-derived macromolecules have established themselves as the
mainstay in protein-based therapeutic molecules (biologics). Our knowledge of the structure …
mainstay in protein-based therapeutic molecules (biologics). Our knowledge of the structure …
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA
Protein–RNA and protein–DNA complexes play critical roles in biology. Despite
considerable recent advances in protein structure prediction, the prediction of the structures …
considerable recent advances in protein structure prediction, the prediction of the structures …
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 …
[HTML][HTML] The HADDOCK2. 2 web server: user-friendly integrative modeling of biomolecular complexes
The prediction of the quaternary structure of biomolecular macromolecules is of paramount
importance for fundamental understanding of cellular processes and drug design. In the era …
importance for fundamental understanding of cellular processes and drug design. In the era …
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 …
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 …
TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning
The cellular immune system, which is a critical component of human immunity, uses T cell
receptors (TCRs) to recognize antigenic proteins in the form of peptides presented by major …
receptors (TCRs) to recognize antigenic proteins in the form of peptides presented by major …
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 …
Predicting protein–protein interactions from the molecular to the proteome level
Identification of protein–protein interactions (PPIs) is at the center of molecular biology
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …