Molecular docking and structure-based drug design

S Agnihotry, RK Pathak, A Srivastav, PK Shukla… - Computer-aided drug …, 2020 - Springer
Computer-aided drug designing (CADD) relates to drug discovery, also characterized as a
cost-effective and active tool that manages or creates theoretical models that would be used …

A protein‐RNA docking benchmark (II): Extended set from experimental and homology modeling data

L Pérez‐Cano, B Jiménez‐García… - Proteins: Structure …, 2012 - Wiley Online Library
We present here an extended protein–RNA docking benchmark composed of 71 test cases
in which the coordinates of the interacting protein and RNA molecules are available from …

Evidence of direct complementary interactions between messenger RNAs and their cognate proteins

AA Polyansky, B Zagrovic - Nucleic acids research, 2013 - academic.oup.com
Recently, the ability to interact with messenger RNA (mRNA) has been reported for a
number of known RNA-binding proteins, but surprisingly also for different proteins without …

[HTML][HTML] Interaction preferences between protein side chains and key epigenetic modifications 5-methylcytosine, 5-hydroxymethycytosine and N6-methyladenine

M Hajnic, S Alonso-Gil, AA Polyansky, A de Ruiter… - Scientific Reports, 2022 - nature.com
Covalent modifications of standard DNA/RNA nucleobases affect epigenetic regulation of
gene expression by modulating interactions between nucleic acids and protein readers. We …

Absolute binding-free energies between standard RNA/DNA nucleobases and amino-acid sidechain analogs in different environments

A de Ruiter, B Zagrovic - Nucleic acids research, 2015 - academic.oup.com
Despite the great importance of nucleic acid–protein interactions in the cell, our
understanding of their physico-chemical basis remains incomplete. In order to address this …

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 …

Chromenopyrazole−Peptide Conjugates as Small‐Molecule Based Inhibitors Disrupting the Protein−RNA Interaction of LIN28‐let‐7

P Hommen, J Hwang, F Huang, L Borgelt… - …, 2023 - Wiley Online Library
Targeting the protein− RNA interaction of LIN28 and let‐7 is a promising strategy for the
development of novel anticancer therapeutics. However, a limited number of small‐molecule …

SPOT-Seq-RNA: predicting protein–RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction

Y Yang, H Zhao, J Wang, Y Zhou - Protein structure prediction, 2014 - Springer
RNA-binding proteins (RBPs) play key roles in RNA metabolism and post-transcriptional
regulation. Computational methods have been developed separately for prediction of RBPs …

[HTML][HTML] RNA 3D structure prediction guided by independent folding of homologous sequences

M Magnus, K Kappel, R Das, JM Bujnicki - BMC bioinformatics, 2019 - Springer
Background The understanding of the importance of RNA has dramatically changed over
recent years. As in the case of proteins, the function of an RNA molecule is encoded in its …

An updated dataset and a structure‐based prediction model for protein–RNA binding affinity

X Hong, X Tong, J Xie, P Liu, X Liu… - Proteins: Structure …, 2023 - Wiley Online Library
Understanding the process of protein–RNA interaction is essential for structural biology. The
thermodynamic process is an important part to uncover the protein–RNA interaction …