FATCAT 2.0: towards a better understanding of the structural diversity of proteins

Z Li, L Jaroszewski, M Iyer, M Sedova… - Nucleic acids …, 2020 - academic.oup.com
Abstract FATCAT 2.0 server (http://fatcat. godziklab. org/), provides access to a flexible
protein structure alignment algorithm developed in our group. In such an alignment …

LncRNA NNT-AS1/hsa-miR-485–5p/HSP90 axis in-silico and clinical prospect correlated-to histologic grades-based CRC stratification: A step toward ncRNA …

NM El-Sheikh, AI Abulsoud, A Fawzy, EF Wasfey… - … -Research and Practice, 2023 - Elsevier
The oncogenic effects of long non-coding RNA (lncRNA) Nicotinamide Nucleotide
Transhydrogenase-antisense RNA1 (NNT-AS1) role in colorectal cancer (CRC) hasn't been …

Nuclear envelope, chromatin organizers, histones, and DNA: The many achilles heels exploited across cancers

AK Balaji, S Saha, S Deshpande, D Poola… - Frontiers in Cell and …, 2022 - frontiersin.org
In eukaryotic cells, the genome is organized in the form of chromatin composed of DNA and
histones that organize and regulate gene expression. The dysregulation of chromatin …

[HTML][HTML] The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine

M Rosas-Lemus, G Minasov, L Shuvalova, NL Inniss… - BioRxiv, 2020 - ncbi.nlm.nih.gov
SARS-CoV-2 is a member of the coronaviridae family and is the etiological agent of the
respiratory Coronavirus Disease 2019. The virus has spread rapidly around the world …

mTM-align: a server for fast protein structure database search and multiple protein structure alignment

R Dong, S Pan, Z Peng, Y Zhang… - Nucleic acids research, 2018 - academic.oup.com
With the rapid increase of the number of protein structures in the Protein Data Bank, it
becomes urgent to develop algorithms for efficient protein structure comparisons. In this …

Cancer-associated circRNA–miRNA–mRNA Regulatory networks: a meta-analysis

S Khan, A Jha, AC Panda, A Dixit - Frontiers in Molecular Biosciences, 2021 - frontiersin.org
Recent advances in sequencing technologies and the discovery of non-coding RNAs
(ncRNAs) have provided new insights in the molecular pathogenesis of cancers. Several …

PDBFlex: exploring flexibility in protein structures

T Hrabe, Z Li, M Sedova, P Rotkiewicz… - Nucleic acids …, 2016 - academic.oup.com
The PDBFlex database, available freely and with no login requirements at http://pdbflex. org,
provides information on flexibility of protein structures as revealed by the analysis of …

Mn2+ coordinates Cap-0-RNA to align substrates for efficient 2′-O-methyl transfer by SARS-CoV-2 nsp16

G Minasov, M Rosas-Lemus, L Shuvalova, NL Inniss… - Science …, 2021 - science.org
Capping of viral messenger RNAs is essential for efficient translation, for virus replication,
and for preventing detection by the host cell innate response system. The SARS-CoV-2 …

Dissecting protein domain variability in the core RNA interference machinery of five insect orders

FBM Arraes, D Martins-de-Sa, DD Noriega Vasquez… - RNA biology, 2021 - Taylor & Francis
ABSTRACT RNA interference (RNAi)-mediated gene silencing can be used to control
specific insect pest populations. Unfortunately, the variable efficiency in the knockdown …

Bioinformatic analysis of the flavin-dependent amine oxidase superfamily: adaptations for substrate specificity and catalytic diversity

MA Tararina, KN Allen - Journal of molecular biology, 2020 - Elsevier
The flavin-dependent amine oxidase (FAO) superfamily consists of over 9000 nonredundant
sequences represented in all domains of life. Of the thousands of members identified, only …