[PDF][PDF] Integrative modeling of biomolecular complexes: HADDOCKing with cryo-electron microscopy data

GCP van Zundert, ASJ Melquiond, AMJJ Bonvin - Structure, 2015 - cell.com
Protein-protein interactions play a central role in all cellular processes. Insight into their
atomic architecture is therefore of paramount importance. Cryo-electron microscopy (cryo …

Profiling the disintegration of BRPs released by massive wasp stings using serratiopeptidase: An in-silico insight

A Dhiman, R Purohit - Computers in Biology and Medicine, 2023 - Elsevier
Serratiopeptidase is a multifaceted therapeutic enzyme renowned for its anti-inflammatory,
analgesic, anti-biofilm, fibrinolytic, and anti-edemic properties. It is vital to uncover more …

[HTML][HTML] Structure of p15PAF–PCNA complex and implications for clamp sliding during DNA replication and repair

A De Biasio, AI De Opakua, GB Mortuza… - Nature …, 2015 - nature.com
The intrinsically disordered protein p15PAF regulates DNA replication and repair by binding
to the proliferating cell nuclear antigen (PCNA) sliding clamp. We present the structure of the …

[PDF][PDF] Structure and mechanism of receptor sharing by the IL-10R2 common chain

S Yoon, BC Jones, NJ Logsdon, BD Harris… - Structure, 2010 - cell.com
IL-10R2 is a shared cell surface receptor required for the activation of five class 2 cytokines
(IL-10, IL-22, IL-26, IL-28, and IL-29) that play critical roles in host defense. To define the …

[HTML][HTML] MARTINI-based protein-DNA coarse-grained HADDOCKing

RV Honorato, J Roel-Touris… - Frontiers in molecular …, 2019 - frontiersin.org
Modeling biomolecular assemblies is an important field in computational structural biology.
The inherent complexity of their energy landscape and the computational cost associated …

[HTML][HTML] Bioinformatics tools and benchmarks for computational docking and 3D structure prediction of RNA-protein complexes

C Nithin, P Ghosh, JM Bujnicki - Genes, 2018 - mdpi.com
RNA-protein (RNP) interactions play essential roles in many biological processes, such as
regulation of co-transcriptional and post-transcriptional gene expression, RNA splicing …

A protein–DNA docking benchmark

M van Dijk, AMJJ Bonvin - Nucleic acids research, 2008 - academic.oup.com
We present a protein–DNA docking benchmark containing 47 unbound–unbound test cases
of which 13 are classified as easy, 22 as intermediate and 12 as difficult cases. The latter …

[HTML][HTML] In silico optimization of RNA–protein interactions for CRISPR-Cas13-based antimicrobials

H Park, Y Park, U Berani, E Bang, J Vankerschaver… - Biology Direct, 2022 - Springer
RNA–protein interactions are crucial for diverse biological processes. In prokaryotes, RNA–
protein interactions enable adaptive immunity through CRISPR-Cas systems. These …

[PDF][PDF] Structural analysis of large protein complexes using solvent paramagnetic relaxation enhancements

T Madl, T Güttler, D Görlich… - Angewandte Chemie …, 2011 - researchgate.net
Understanding the function of biomolecular complexes requires their structural analysis at
atomic resolution. To solve high-resolution structures by abinitio calculations typically data …

Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins

M Vanmeert, J Razzokov, MU Mirza… - Nucleic Acids …, 2019 - academic.oup.com
Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be
used for the storage of genetic information. In vivo XNA applications could be developed into …