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R2DT is a framework for predicting and visualising RNA secondary structure using templates

Authors: 
Blake A. Sweeney, David Hoksza, Eric P. Nawrocki, Carlos Eduardo Ribas, Fábio Madeira, Jamie J. Cannone, Robin Gutell, Aparna Maddala, Caeden D. Meade, Loren Dean Williams, Anton S. Petrov, Patricia P. Chan, Todd M. Lowe, Robert D. Finn, Anton I. Petrov
Indexed by WOS: 
Indexed by WOS
Indexed by SCOPUS: 
Indexed by SCOPUS
Type: 
Journal
State: 
Published
Language: 
EN
Conference/Journal name: 
Nature communications
Publisher: 
Nature
Year: 
2021
Volume: 
12
Issue: 
3494
ISSN: 
2041-1723
DOI: 
https://doi.org/10.1038/s41467-021-23555-5

MolArt

Type: 
Bioinformatics & Cheminformatics
One line description: 
MolArt is a responsive, easy-to-use JavaScript plugin which enables users to view annotated protein sequence and overlay the annotations over a corresponding experimental or predicted protein structure.
HTML link: 
https://github.com/cusbg/MolArt
Annotation: 

MolArt is a responsive, easy-to-use JavaScript plugin which enables users to view annotated protein sequence (including variation data from large scale studies) and overlay the annotations over a corresponding experimental or predicted protein structure. It couples protein sequence annotation capabilities provided by ProtVista (or more precisely its modified responsive version implemented when developing MolArt) with structure visualization capabilities provided by LiteMol. Since it does not have any software dependencies and all the data are obtained on the fly, it is easy to integrate it to any web page.

Developers: 
david.hoksza

Traveler

Type: 
Bioinformatics & Cheminformatics
One line description: 
Traveler is an RNA sescondary structure visualization tool implementing a template-based approach enabling to lay out even the largest RNA structures in the standard orientation.
HTML link: 
https://github.com/cusbg/traveler
Annotation: 

Visualization of RNA secondary structures is a complex task, and, especially in the case of large RNA structures where the expected layout is largely habitual, the existing visualization tools often fail to produce suitable visualizations. This led us to the idea to use existing layouts as templates for the visualization of new RNAs similarly to how templates are used in homology-based structure prediction.

Traveler is a software tool enabling visualization of a target RNA secondary structure using an existing layout of a sufficiently similar RNA structure as a template. Traveler is based on an algorithm which converts the target and template structures into corresponding tree representations and utilizes tree edit distance coupled with layout modification operations to transform the template layout into the target one. Traveler thus accepts a pair of secondary structures and a template layout and outputs a layout for the target structure.

Traveler is used by RNACentral for visualization of all the secondary structures available in RNACentral. 

 

Developers: 
david.hoksza

Active sites detection

Research area: 
Bioinformatics & Cheminformatics

Macromolecules such as proteins, DNA or RNA perform many different biological functions and so ensure most of the vital processes in living organisms. The protein function is determined by its interaction with other molecules and thus detection of regions where protein interacts and how the interaction is carried out finds application in many areas including drug development. In this field, we mostly focus on the detection of active sites from protein 3D structures.

Visualization

Research area: 
Bioinformatics & Cheminformatics

In the visualization domain, we develop both algorithms for visualization of non-trivial data types and web-based tools for visualization of molecular structure information. Our aim is not only to come up with new visualization approaches but also to go the last mile and develop complete software solutions.

RNAcentral 2021: secondary structure integration, improved sequence search, and new member databases

Authors: 
David Hoksza, RNAcentral Consoritum
Indexed by WOS: 
Indexed by WOS
Indexed by SCOPUS: 
Indexed by SCOPUS
Type: 
Journal
State: 
Accepted
Language: 
EN
Conference/Journal name: 
Nucleic Acids Research
Publisher: 
Oxford Journals
Year: 
2020
ISSN: 
1362-4962
DOI: 
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa921/5940500

Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants

Authors: 
Sumaiya Iqbal, Eduardo Pérez-Palma, Jakob Berg Jespersen, Patrick May, David Hoksza, Henrike O. Heyne, Shehab S. Ahmed, Zaara T. Rifat, M Sohel Rahman, Kasper Lage, Aarno Palotie, Jeffrey R. Cottrell, Florence F. Wagner, Mark J. Daly, Arthur J Campbell, Dennis Lal
Indexed by WOS: 
Indexed by WOS
Indexed by SCOPUS: 
Indexed by SCOPUS
Type: 
Journal
State: 
Accepted
Language: 
EN
Conference/Journal name: 
Proceedings of the National Academy of Sciences of the United States of America (PNAS)
Publisher: 
United States National Academy of Sciences
Year: 
2020
ISSN: 
1091-6490
DOI: 
https://www.pnas.org/content/early/2020/10/23/2002660117

Disease and pathway maps for Rare Diseases

Authors: 
Piotr Gawron, David Hoksza, Janet Pinero, Maria Pena Chilet, Marina Esteban Jose Luis Fernandez, Vincenza Colonna, Joaquin Dopazo, Laura I. Furlong, Marek Ostaszewski
Indexed by WOS: 
Not indexed by WOS
Indexed by SCOPUS: 
Not indexed by SCOPUS
Type: 
Proceedings
State: 
Published
Language: 
EN
Conference/Journal name: 
BioHackathon series: BioHackathon EUROPE, 2019
Publisher: 
biohackrxiv
Year: 
2020
Location: 
Paris, France
DOI: 
https://doi.org/10.37044/osf.io/gmbjv

MISCAST: MIssense variant to protein StruCture Analysis web SuiTe

Authors: 
Sumaiya Iqbal, David Hoksza, Eduardo Perez-Palma, Patrick May, Jakob Berg Jespersen, Shehab Sarar Ahmed, Zaara Tasnim Rifat, Henrike O. Heyne, M. Sohel Rahman, Je rey R. Cottrell, Florence F. Wagner, Mark J. Daly, Arthur J. Campbell and Dennis Lal
Indexed by WOS: 
Indexed by WOS
Indexed by SCOPUS: 
Indexed by SCOPUS
Type: 
Journal
State: 
Accepted
Language: 
EN
Conference/Journal name: 
Nucleic Acids Research
Publisher: 
Oxford Journals
Year: 
2020
Volume: 
48
Issue: 
W1
Pages: 
W132–W139
ISSN: 
1362-4962
DOI: 
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa361/5836773

Towards evaluating and simulating keyword queries for development of interactive known-item search systems

Authors: 
Ladislav Peška, František Mejzlík, Tomáš Souček, Jakub Lokoč
Indexed by WOS: 
Not indexed by WOS
Indexed by SCOPUS: 
Not indexed by SCOPUS
Type: 
Proceedings
State: 
Accepted
Language: 
EN
Conference/Journal name: 
ICMR 2020
Publisher: 
ACM
Year: 
2020
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by Dr. Radut.