RNA‐protein interactions in an unstructured context

B Zagrovic, L Bartonek, AA Polyansky - FEBS letters, 2018 - Wiley Online Library
Despite their importance, our understanding of noncovalent RNA–protein interactions is
incomplete. This especially concerns the binding between RNA and unstructured protein …

[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 …

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein–RNA complexes

F Chen, H Sun, J Wang, F Zhu, H Liu, Z Wang, T Lei… - Rna, 2018 - rnajournal.cshlp.org
Molecular docking provides a computationally efficient way to predict the atomic structural
details of protein–RNA interactions (PRI), but accurate prediction of the three-dimensional …

Protein–RNA interactions: structural characteristics and hotspot amino acids

DM Krüger, S Neubacher, TN Grossmann - Rna, 2018 - rnajournal.cshlp.org
Structural information about protein–RNA complexes supports the understanding of crucial
recognition processes in the cell, and it can allow the development of high affinity ligands to …

Weak IgG self‐and hetero‐association characterized by fluorescence analytical ultracentrifugation

D Yang, JJ Correia, WF Stafford III, CJ Roberts… - Protein …, 2018 - Wiley Online Library
Weak protein–protein interactions may be important to binding cooperativity. A panel of
seven fluorescently labeled tracer monoclonal IgG antibodies, differing in variable (V) and …

[HTML][HTML] Molecular modeling applied to nucleic acid-based molecule development

A Krüger, FM Zimbres, T Kronenberger, C Wrenger - Biomolecules, 2018 - mdpi.com
Molecular modeling by means of docking and molecular dynamics (MD) has become an
integral part of early drug discovery projects, enabling the screening and enrichment of large …

3dRPC: a web server for 3D RNA–protein structure prediction

Y Huang, H Li, Y Xiao - Bioinformatics, 2018 - academic.oup.com
RNA–protein interactions occur in many biological processes. To understand the
mechanism of these interactions one needs to know three-dimensional (3D) structures of …

[HTML][HTML] Deciphering RNA-recognition patterns of intrinsically disordered proteins

A Srivastava, S Ahmad, MM Gromiha - International journal of molecular …, 2018 - mdpi.com
Intrinsically disordered regions (IDRs) and protein (IDPs) are highly flexible owing to their
lack of well-defined structures. A subset of such proteins interacts with various substrates; …

Protein-RNA docking using ICM

YA Arnautova, R Abagyan, M Totrov - Journal of Chemical Theory …, 2018 - ACS Publications
Protein-RNA interactions play an important role in many biological processes.
Computational methods such as docking have been developed to complement existing …

Inhibition of protein interactions: co-crystalized protein–protein interfaces are nearly as good as holo proteins in rigid-body ligand docking

S Belkin, PJ Kundrotas, IA Vakser - Journal of computer-aided molecular …, 2018 - Springer
Modulating protein interaction pathways may lead to the cure of many diseases. Known
protein–protein inhibitors bind to large pockets on the protein–protein interface. Such large …