Results 91 to 100 of about 9,562,225 (293)

Prediction of RNA Secondary Structure Using Butterfly Optimization Algorithm

Human-Centric Intelligent Systems
Ribonucleic acid (RNA) structure is vital to its ability to function within the cell. The ability to predict RNA structure is essential to implementing new medications and understanding genetic illnesses.
Sajib Chatterjee, Rameswar Debnath, Sujit Biswas, Anupam Kumar Bairagi   +3 more
doaj   +1 more source

RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks

, 2021
RNA three-dimensional structure prediction has been relied on using a predicted or experimentally determined secondary structure as a restraint to reduce the conformational sampling space. However, the secondary-structure restraints are limited to paired
Singh, Jaspreet, Zhou, Yaoqi, Paliwal, Kuldip, Singh, Jaswinder, Jaswinder Singh, Jaspreet Singh, Yaoqi Zhou, Kuldip Paliwal   +7 more
core   +1 more source

SPHINX31 acts as a SRPK1 inhibitor targeting the ATR/DNA‐PKcs/CHK1 replicative checkpoint to inhibit cell growth in non‐small cell lung cancer

Molecular Oncology, EarlyView.
The kinase SRPK1 directly interacts with the protein TOPBP1 and regulates the pre‐mRNA splicing of WIZ thereby contributing to the activation of the ATR/CHK1 replicative checkpoint in response to replicative stress. This allows cancer cells' genomic stability and survival.
Amani Shreim, Aurelie Genoux, Nadiia Zubchuk, Haoyang Zheng, Perla Salameh, Theo Ziegelmeyer, Fabien Dalonneau, Margot Rouchette, Christiane Oddou, Simona Miron, Helene Polveche, Adiilah Mamode Cassim, Carmen Garrido, Eleni Nikolakaki, Didier Auboeuf, Tao Jia, Sophie Zinn‐Justin, Beatrice Eymin   +17 more
wiley   +1 more source

Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling

, 2022
MOTIVATION: Recently, AlphaFold2 achieved high experimental accuracy for the majority of proteins in Critical Assessment of Structure Prediction (CASP 14).
Singh, Jaspreet, Zhou, Yaoqi, Litfin, Thomas, Paliwal, Kuldip, Singh, Jaswinder, Jaswinder Singh, Thomas Litfin, Jaspreet Singh, Yaoqi Zhou, Kuldip Paliwal   +9 more
core   +1 more source

Mutant p53R273H disrupts PDPK1 homodimerization and contributes to PDPK1 activation

Molecular Oncology, EarlyView.
How mutant p53R273H drives AKT signaling is unclear. We show that p53R273H, but not wild‐type, directly binds PDPK1 via a mutation‐dependent conformational change. This interaction disrupts inhibitory PDPK1 homodimerization and enhances AKT phosphorylation.
Mei Chee Lim, Alvin Kunyao Guo, Yoko Itahana, Srinivasaraghavan Kannan, Valerie Goh, Mingmin Ong, Terina Yan Wen Tay, Weiying Ye, Sabhashina Radha Krishnan, Jun Nishiyama, Chandra S Verma, Koji Itahana   +11 more
wiley   +1 more source

RNAalifold: improved consensus structure prediction for RNA alignments

BMC Bioinformatics, 2008
Background The prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a set of aligned sequences, is one ...
Stadler Peter F, Gruber Andreas R, Will Sebastian, Hofacker Ivo L, Bernhart Stephan H   +4 more
doaj   +1 more source

Shape based indexing for faster search of RNA family databases [PDF]

, 2008
Janssen S, Reeder J, Giegerich R. Shape based indexing for faster search of RNA family databases. BMC Bioinformatics. 2008;9(1):131.Background: Most non-coding RNA families exert their function by means of a conserved, common secondary structure.
Janssen Stefan, Reeder Jens, Janssen, Stefan ; https://orcid.org/, Reeder, Jens, Giegerich, Robert, Giegerich Robert   +5 more
core   +1 more source

Targeting the EpCAM‐AXL axis to overcome drug resistance in lung cancer

Molecular Oncology, EarlyView.
Lung cancer cells often evade therapy by hijacking signaling pathways. We reveal that cleaved EpCAM (sEpCAM) stabilizes the oncogenic protein AXL, driving NF‐κB and STAT3‐mediated chemoresistance. This EpCAM‐AXL axis identifies a high‐risk patient subset with poor prognosis.
Alexa Guerrero‐Alba, Mark Shacker, Timothy P. Fleming, Michael A. Smith, Ross M. Bremner, Narendra V. Sankpal   +5 more
wiley   +1 more source

A Method to Predict the Structure and Stability of RNA/RNA Complexes [PDF]

, 2016
RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation
Xiaojun, Xu, Shi-Jie, Chen
openaire   +2 more sources

Characterization of therapeutic antibodies targeting lymphatic and vascular resistance factor for the treatment of hypervascularized and highly metastatic cancers

Molecular Oncology, EarlyView.
LVRF (lymphatic and vascular resistance factor) is a VEGFA splice variant upregulated in response to anti‐angiogenic therapy that fosters tumor adaptation through enhanced vascularization, lymphangiogenesis, and metastatic dissemination. Targeting LVRF with fully human neutralizing antibodies disrupts these processes and limits resistant tumor growth ...
Marion David, Arthur Karaulic, Audrey Bennetot, Clémence Fournier, Quentin Odet, Arthur Gouraud, Isabelle Bourget, Cédric Gaggioli, Sandy Giuliano, Frédéric Luciano, Olivier Léger, Zaki Sellam, Gilles Pagès   +12 more
wiley   +1 more source