Software for molecular docking: a review

NS Pagadala, K Syed, J Tuszynski - Biophysical reviews, 2017 - Springer
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 …

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 …

Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA

M Baek, R McHugh, I Anishchenko, H Jiang, D Baker… - Nature …, 2024 - nature.com
Protein–RNA and protein–DNA complexes play critical roles in biology. Despite
considerable recent advances in protein structure prediction, the prediction of the structures …

The ClusPro web server for protein–protein docking

D Kozakov, DR Hall, B **a, KA Porter, D Padhorny… - Nature protocols, 2017 - nature.com
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 …

[HTML][HTML] The HADDOCK2. 2 web server: user-friendly integrative modeling of biomolecular complexes

GCP Van Zundert, J Rodrigues, M Trellet… - Journal of molecular …, 2016 - Elsevier
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 …

Coarse-grained protein models and their applications

S Kmiecik, D Gront, M Kolinski, L Wieteska… - Chemical …, 2016 - ACS Publications
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 …

New additions to the C lus P ro server motivated by CAPRI

S Vajda, C Yueh, D Beglov, T Bohnuud… - Proteins: Structure …, 2017 - Wiley Online Library
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 …

TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning

R Yin, HV Ribeiro-Filho, V Lin… - Nucleic Acids …, 2023 - academic.oup.com
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 …

Performance and its limits in rigid body protein-protein docking

IT Desta, KA Porter, B **a, D Kozakov, S Vajda - Structure, 2020 - cell.com
The development of fast Fourier transform (FFT) algorithms enabled the sampling of billions
of complex conformations and thus revolutionized protein-protein docking. FFT-based …

Predicting protein–protein interactions from the molecular to the proteome level

O Keskin, N Tuncbag, A Gursoy - Chemical reviews, 2016 - ACS Publications
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 …