Results 131 to 140 of about 1,677,396 (366)

RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning

BMC Bioinformatics, 2018
Background Protein dihedral angles provide a detailed description of protein local conformation. Predicted dihedral angles can be used to narrow down the conformational space of the whole polypeptide chain significantly, thus aiding protein tertiary ...
Yujuan Gao, Sheng Wang, Minghua Deng, Jinbo Xu   +3 more
doaj   +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

Multidimensional OMICs reveal ARID1A orchestrated control of DNA damage, splicing, and cell cycle in normal‐like and malignant urothelial cells

Molecular Oncology, EarlyView.
Loss of the frequently mutated chromatin remodeler ARID1A, a subunit of the SWI/SNF cBAF complex, results in less open chromatin, alternative splicing, and the failure to stop cells from progressing through the cell cycle after DNA damage in bladder (cancer) cells. Created in BioRender. Epigenetic regulators, such as the SWI/SNF complex, with important
Rebecca M. Schlösser, Florian Krumbach, Eyleen Corrales, Geoffroy Andrieux, Christian Preisinger, Franziska Liss, Alexandra Golzmann, Melanie Boerries, Kerstin Becker, Ruth Knüchel, Stefan Garczyk, Bernhard Lüscher   +11 more
wiley   +1 more source

DeepCDpred: Inter-residue distance and contact prediction for improved prediction of protein structure.

PLoS ONE, 2019
Rapid, accurate prediction of protein structure from amino acid sequence would accelerate fields as diverse as drug discovery, synthetic biology and disease diagnosis.
Shuangxi Ji, Tuğçe Oruç, Liam Mead, Muhammad Fayyaz Rehman, Christopher Morton Thomas, Sam Butterworth, Peter James Winn   +6 more
doaj   +1 more source

ShcD adaptor protein drives invasion of triple negative breast cancer cells by aberrant activation of EGFR signaling

Molecular Oncology, EarlyView.
We identified adaptor protein ShcD as upregulated in triple‐negative breast cancer and found its expression to be correlated with reduced patient survival and increased invasion in cell models. Using a proteomic screen, we identified novel ShcD binding partners involved in EGFR signaling pathways.
Hayley R. Lau, Hayley S. Smith, Begüm Alural, Claire E. Martin, Laura A. New, Manali Tilak, Sara L. Banerjee, Hannah N. Robeson, Nicolas Bisson, Anne‐Claude Gingras, Jasmin Lalonde, Nina Jones   +11 more
wiley   +1 more source

Limitations of Protein Structure Prediction Algorithms in Therapeutic Protein Development

BioMedInformatics
The three-dimensional protein structure is pivotal in comprehending biological phenomena. It directly governs protein function and hence aids in drug discovery. The development of protein prediction algorithms, such as AlphaFold2, ESMFold, and trRosetta,
Sarfaraz K. Niazi, Zamara Mariam, Rehan Z. Paracha   +2 more
doaj   +1 more source

Hill-Climbing search and diversification within an evolutionary approach to protein structure prediction

BioData Mining, 2011
Proteins are complex structures made of amino acids having a fundamental role in the correct functioning of living cells. The structure of a protein is the result of the protein folding process.
Chira Camelia, Horvath Dragos, Dumitrescu D   +2 more
doaj   +1 more source

Local Backbone Structure Prediction of Proteins

In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation, 2004
A statistical analysis of the PDB structures has led us to define a new set of small 3D structural prototypes called Protein Blocks (PBs). This structural alphabet includes 16 PBs, each one is defined by the (Φ, Ψ) dihedral angles of 5 consecutive residues.
de Brevern, Alexandre, Benros, Cristina, Gautier, Romain, Valadié, Hélène, Hazout, Serge, Etchebest, Catherine   +5 more
openaire   +3 more sources

Ubiquitination of transcription factors in cancer: unveiling therapeutic potential

Molecular Oncology, EarlyView.
In cancer, dysregulated ubiquitination of transcription factors contributes to the uncontrolled growth and survival characteristics of tumors. Tumor suppressors are degraded by aberrant ubiquitination, or oncogenic transcription factors gain stability through ubiquitination, thereby promoting tumorigenesis.
Dongha Kim, Hye Jin Nam, Sung Hee Baek
wiley   +1 more source

Determination of ADP/ATP translocase isoform ratios in malignancy and cellular senescence

Molecular Oncology, EarlyView.
The individual functions of three isoforms exchanging ADP and ATP (ADP/ATP translocases; ANTs) on the mitochondrial membrane remain unclear. We developed a method for quantitatively differentiating highly similar human ANT1, ANT2, and ANT3 using parallel reaction monitoring. This method allowed us to assess changes in translocase levels during cellular
Zuzana Liblova, Dominika Maurencova, Barbora Salovska, Marek Kratky, Tomas Mracek, Zuzana Korandova, Alena Pecinova, Pavla Vasicova, David Rysanek, Ladislav Andera, Ivo Fabrik, Rudolf Kupcik, Pavel Kashmel, Pinky Sultana, Vojtech Tambor, Jiri Bartek, Josef Novak, Marie Vajrychova, Zdenek Hodny   +18 more
wiley   +1 more source