Protein-protein docking: From interaction to interactome

IA Vakser - Biophysical journal, 2014 - cell.com
The protein-protein docking problem is one of the focal points of activity in computational
biophysics and structural biology. The three-dimensional structure of a protein-protein …

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 …

[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 …

Sequence co-evolution gives 3D contacts and structures of protein complexes

TA Hopf, CPI Schärfe, JP Rodrigues, AG Green… - elife, 2014 - elifesciences.org
Protein–protein interactions are fundamental to many biological processes. Experimental
screens have identified tens of thousands of interactions, and structural biology has …

Predicting the zoonotic capacity of mammals to transmit SARS-CoV-2

IR Fischhoff, AA Castellanos… - … of the Royal …, 2021 - royalsocietypublishing.org
Back and forth transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-
2) between humans and animals will establish wild reservoirs of virus that endanger long …

Antibody specific B-cell epitope predictions: leveraging information from antibody-antigen protein complexes

MC Jespersen, S Mahajan, B Peters… - Frontiers in …, 2019 - frontiersin.org
B-cells can neutralize pathogenic molecules by targeting them with extreme specificity using
receptors secreted or expressed on their surface (antibodies). This is achieved via molecular …

Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking

Y Yan, Z Wen, X Wang… - … : Structure, Function, and …, 2017 - Wiley Online Library
Protein–protein docking is an important computational tool for predicting protein–protein
interactions. With the rapid development of proteomics projects, more and more …

A 3D structural SARS-CoV-2–human interactome to explore genetic and drug perturbations

SD Wierbowski, S Liang, Y Liu, Y Chen, S Gupta… - Nature …, 2021 - nature.com
Emergence of new viral agents is driven by evolution of interactions between viral proteins
and host targets. For instance, increased infectivity of SARS-CoV-2 compared to SARS-CoV …

[图书][B] From protein structure to function with bioinformatics

DJ Rigden, DJ Rigden - 2009 - Springer
With the success of an expanding array of genome sequencing projects, the number of
known protein sequences has been increasing exponentially. However, the sequences on …

Assessment of the CASP14 assembly predictions

B Ozden, A Kryshtafovych… - … : Structure, Function, and …, 2021 - Wiley Online Library
In CASP14, 39 research groups submitted more than 2500 3D models on 22 protein
complexes. In general, the community performed well in predicting the fold of the assemblies …