COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures

GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA

The GrAfSS (Graph theoretical Applications for Substructure Searching) webserver is a platform to search for three-dimensional substructures of: (i) amino acid side chains in protein structures; and (ii) base arrangements in RNA structures. The webserver interfaces the functions of five different graph theoretical algorithms – ASSAM, SPRITE, IMAAAGINE, NASSAM and COGNAC – into a single substructure searching suite. Users will be able to identify whether a three-dimensional (3D) arrangement of interest, such as a ligand binding site or 3D motif, observed in a protein or RNA structure can be found in other structures available in the Protein Data Bank (PDB). The webserver also allows users to determine whether a protein or RNA structure of interest contains substructural arrangements that are similar to known motifs or 3D arrangements. These capabilities allow for the functional annotation of new structures that were either experimentally determined or computationally generated (such as the coordinates generated by AlphaFold2) and can provide further insights into the diversity or conservation of functional mechanisms of structures in the PDB. The computed substructural superpositions are visualized using integrated NGL viewers. The GrAfSS server is available at http://mfrlab.org/grafss/.

Features and Functions of the A-Minor Motif, the Most Common Motif in RNA Structure

A-minor motifs are RNA tertiary structure motifs that generally involve a canonical base pair and an adenine base forming hydrogen bonds with the minor groove of the base pair. Such motifs are among the most common tertiary interactions in known RNA structures, comparable in number with the non-canonical base pairs. They are often found in functionally important regions of non-coding RNAs and, in particular, play a central role in protein synthesis. Here, we review local variations of the A-minor geometry and discuss difficulties associated with their annotation, as well as various structural contexts and common A-minor co-motifs, and diverse functions of A-minors in various processes in a living cell.

Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures

The increasing number and complexity of structures containing RNA chains in the Protein Data Bank (PDB) have led to the need for automated structure annotation methods to replace or complement expert visual curation. This is especially true when searching for tertiary base motifs and substructures. Such base arrangements and motifs have diverse roles that range from contributions to structural stability to more direct involvement in the molecule's functions, such as the sites for ligand binding and catalytic activity. We review the utility of computational approaches in annotating RNA tertiary base motifs in a dataset of PDB structures, particularly the use of graph theoretical algorithms that can search for such base motifs and annotate them or find and annotate clusters of hydrogen-bond-connected bases. We also demonstrate how such graph theoretical algorithms can be integrated into a workflow that allows for functional analysis and comparisons of base arrangements and sub-structures, such as those involved in ligand binding. The capacity to carry out such automatic curations has led to the discovery of novel motifs and can give new context to known motifs as well as enable the rapid compilation of RNA 3D motifs into a database.

LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor

Protein dynamics is central to all biological processes, including signal transduction, cellular regulation and biological catalysis. Among them, in-depth exploration of ligand-driven protein dynamics contributes to an optimal understanding of protein function, which is particularly relevant to drug discovery. Hence, a wide range of computational tools have been designed to investigate the important dynamic information in proteins. However, performing and analyzing protein dynamics is still challenging due to the complicated operation steps, giving rise to great difficulty, especially for nonexperts. Moreover, there is a lack of web protocol to provide online facility to investigate and visualize ligand-driven protein dynamics. To this end, in this study, we integrated several bioinformatic tools to develop a protocol, named Ligand and Receptor Molecular Dynamics (LARMD, http://chemyang.ccnu.edu.cn/ccb/server/LARMD/ and http://agroda.gzu.edu.cn:9999/ccb/server/LARMD/), for profiling ligand-driven protein dynamics. To be specific, estrogen receptor (ER) was used as a case to reveal ERβ-selective mechanism, which plays a vital role in the treatment of inflammatory diseases and many types of cancers in clinical practice. Two different residues (Ile373/Met421 and Met336/Leu384) in the pocket of ERβ/ERα were the significant determinants for selectivity, especially Met336 of ERβ. The helix H8, helix H11 and H7-H8 loop influenced the migration of selective agonist (WAY-244). These computational results were consistent with the experimental results. Therefore, LARMD provides a user-friendly online protocol to study the dynamic property of protein and to design new ligand or site-directed mutagenesis.

Identification of Structural Motifs Using Networks of Hydrogen-Bonded Base Interactions in RNA Crystallographic Structures

RNA structural motifs can be identified using methods that analyze base–base interactions and the conformation of a structure’s backbone; however, these approaches do not necessarily take into consideration the hydrogen bonds that connect the bases or the networks of inter-connected hydrogen-bonded bases that are found in RNA structures. Large clusters of RNA bases that are tightly inter-connected by a network of hydrogen bonds are expected to be stable and relatively rigid substructures. Such base arrangements could therefore be present as structural motifs in RNA structures, especially when there is a requirement for a highly stable support platform or substructure to ensure the correct folding and spatial maintenance of functional sites that partake in catalysis or binding interactions. In order to test this hypothesis, we conducted a search in available RNA crystallographic structures in the Protein Data Bank database using queries that searched for profiles of bases inter-connected by hydrogen bonds. This method of searching does not require to have prior knowledge of the arrangement being searched. Our search results identified two clusters of six bases that are inter-connected by a network of hydrogen bonds. These arrangements of base sextuples have never been previously reported, thus making this the first report that proposes them as novel RNA tertiary motifs.

Structural database resources for biological macromolecules

This Briefing reviews the widely used, currently active, up-to-date databases derived from the worldwide Protein Data Bank (PDB) to facilitate browsing, finding and exploring its entries. These databases contain visualization and analysis tools tailored to specific kinds of molecules and interactions, often including also complex metrics precomputed by experts or external programs, and connections to sequence and functional annotation databases. Importantly, updates of most of these databases involves steps of curation and error checks based on specific expertise about the subject molecules or interactions, and removal of sequence redundancy, both leading to better data sets for mining studies compared with the full list of raw PDB entries. The article presents the databases in groups such as those aimed to facilitate browsing through PDB entries, their molecules and their general information, those built to link protein structure with sequence and dynamics, those specific for transmembrane proteins, nucleic acids, interactions of biomacromolecules with each other and with small molecules or metal ions, and those concerning specific structural features or specific protein families. A few webservers directly connected to active databases, and a few databases that have been discontinued but would be important to have back, are also briefly commented on. Along the Briefing, sample cases where these databases have been used to aid structural studies or advance our knowledge about biological macromolecules are referenced. A few specific examples are also given where using these databases is easier and more informative than using raw PDB data.

Chemoinformatics at the University of Sheffield 2002-2014

This paper summarises work in chemoinformatics carried out in the Information School of the University of Sheffield during the period 2002-2014. Research studies are described on fingerprint-based similarity searching, data fusion, applications of reduced graphs and pharmacophore mapping, and on the School's teaching in chemoinformatics.

InterRNA: a database of base interactions in RNA structures

A major component of RNA structure stabilization are the hydrogen bonded interactions between the base residues. The importance and biological relevance for large clusters of base interactions can be much more easily investigated when their occurrences have been systematically detected, catalogued and compared. In this paper, we describe the database InterRNA (INTERactions in RNA structures database—http://mfrlab.org/interrna/) that contains records of known RNA 3D motifs as well as records for clusters of bases that are interconnected by hydrogen bonds. The contents of the database were compiled from RNA structural annotations carried out by the NASSAM (http://mfrlab.org/grafss/nassam) and COGNAC (http://mfrlab.org/grafss/cognac) computer programs. An analysis of the database content and comparisons with the existing corpus of knowledge regarding RNA 3D motifs clearly show that InterRNA is able to provide an extension of the annotations for known motifs as well as able to provide novel interactions for further investigations.