Results 131 to 140 of about 18,469,580 (392)

New alphabet-dependent morphological transition in a random RNA alignment

, 2012
We study the fraction $f$ of nucleotides involved in the formation of a cactus--like secondary structure of random heteropolymer RNA--like molecules.
A. Yu. Grosberg, M. V. Tamm, O. V. Valba, S. K. Nechaev, S. K. Lando   +4 more
core   +1 more source

Targeting the MDM2‐MDM4 interaction interface reveals an otherwise therapeutically active wild‐type p53 in colorectal cancer

Molecular Oncology, EarlyView.
This study investigates an alternative approach to reactivating the oncosuppressor p53 in cancer. A short peptide targeting the association of the two p53 inhibitors, MDM2 and MDM4, induces an otherwise therapeutically active p53 with unique features that promote cell death and potentially reduce toxicity towards proliferating nontumor cells.
Sonia Valentini, Giada Mele, Marika Attili, Maria Rita Assenza, Fulvio Saccoccia, Francesca Sardina, Cinzia Rinaldo, Roberto Massari, Nicola Tirelli, Alfredo Pontecorvi, Fabiola Moretti   +10 more
wiley   +1 more source

Ground state and glass transition of the RNA secondary structure

, 2006
RNA molecules form a sequence-specific self-pairing pattern at low temperatures. We analyze this problem using a random pairing energy model as well as a random sequence model that includes a base stacking energy in favor of helix propagation.
Bundschuh, Bundschuh, Carpentier, Dill, Gennes, Halpin-Healy, Hartmann, Higgs, Hwa, Hwa, Isaacs, Jr, Jr, Karlin, Krzakala, L.-H. Tang, Lässig, Marinari, Mukhopadhyay, Mézard, Nussinov, Onuchic, Pagnani, S. Hui, Schueler-Furman, Shakhnovich, Snow, Tang, Tang, Yu, Zeng, Zuker   +31 more
core   +1 more source

SOSUI: classification and secondary structure prediction system for membrane proteins

Bioinform., 1998
UNLABELLED The system SOSUI for the discrimination of membrane proteins and soluble ones together with the prediction of transmembrane helices was developed, in which the accuracy of the classification of proteins was 99% and the corresponding value for ...
T. Hirokawa, Seah Boon-Chieng, S. Mitaku
semanticscholar   +1 more source

Comparing self‐reported race and genetic ancestry for identifying potential differentially methylated sites in endometrial cancer: insights from African ancestry proportions using machine learning models

Molecular Oncology, EarlyView.
Integrating ancestry, differential methylation analysis, and machine learning, we identified robust epigenetic signature genes (ESGs) and Core‐ESGs in Black and White women with endometrial cancer. Core‐ESGs (namely APOBEC1 and PLEKHG5) methylation levels were significantly associated with survival, with tumors from high African ancestry (THA) showing ...
Huma Asif, J. Julie Kim
wiley   +1 more source

SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments

Comput. Appl. Biosci., 1995
Recently a new method called the self-optimized prediction method (SOPM) has been described to improve the success rate in the prediction of the secondary structure of proteins.
C. Geourjon, G. Deléage
semanticscholar   +1 more source

The atypical KRASQ22K mutation directs TGF‐β response towards partial epithelial‐to‐mesenchymal transition in patient‐derived colorectal cancer tumoroids

Molecular Oncology, EarlyView.
TGF‐β has a complex role in cancer, exhibiting both tumor‐suppressive and tumor‐promoting properties. Using a series of differentiated tumoroids, derived from different stages and mutational background of colorectal cancer patients, we replicate this duality of TGF‐β in vitro. Notably, the atypical but highly aggressive KRASQ22K mutation rendered early‐
Theresia Mair, Philip König, Milena Mijović, Jessica Kalla, Anil Baskan, Loan Tran, Kristina Draganić, Pedro Morata Saldaña, Carlos Uziel Pérez Malla, Janette Pfneissl, Andreas Tiefenbacher, Julijan Kabiljo, Velina S. Atanasova, Lisa Wozelka‐Oltjan, Leonhard Müllauer, Michael Bergmann, Raheleh Sheibani‐Tezerji, Gerda Egger   +17 more
wiley   +1 more source

Escape from TGF‐β‐induced senescence promotes aggressive hallmarks in epithelial hepatocellular carcinoma cells

Molecular Oncology, EarlyView.
Chronic TGF‐β exposure drives epithelial HCC cells from a senescent state to a TGF‐β resistant mesenchymal phenotype. This transition is characterized by the loss of Smad3‐mediated signaling, escape from senescence, enhanced invasiveness and metastatic potential, and upregulation of key resistance modulators such as MARK1 and GRM8, ultimately promoting
Minenur Kalyoncu, Dilara Demirci, Sude Eris, Bengisu Dayanc, Ece Cakiroglu, Merve Basol, Merve Uysal, Gulcin Cakan‐Akdogan, Fang Liu, Mehmet Ozturk, Gökhan Karakülah, Serif Senturk   +11 more
wiley   +1 more source

Recoverable One-dimensional Encoding of Three-dimensional Protein Structures

, 2005
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence.
A. R. Kinjo, Berman, Havel, K. Nishikawa, Kabsch, Kinjo, Nakai, Plaxco, Porto, Vendruscolo, Wang   +10 more
core   +2 more sources

Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function

PLoS Genetics, 2015
Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity.
Cristian Del Campo, Alexander Bartholomäus, I. Fedyunin, Z. Ignatova   +3 more
semanticscholar   +1 more source