Results 91 to 100 of about 1,402,076 (343)

Competitive ligand binding kinetics to linear polymers [PDF]

Physical Review E 107, 024401 (2023)
Different types of ligands compete in binding to polymers with different consequences for the physical and chemical properties of the resulting complex. Here, we derive a general kinetic model for the competitive binding kinetics of different types of ligands to a linear polymer, using the McGhee and von Hippel detailed binding site counting procedure.
arxiv   +1 more source

The Saccharomyces cerevisiae amino acid transporter Lyp1 has a broad substrate spectrum

FEBS Letters, EarlyView.
In Saccharomyces cerevisiae, Yeast Amino acid Transporter family members mediate the import of amino acids, ranging from substrate specialists to generalists. Here, we show that the specialist transporter, Lyp1, has a broader substrate spectrum than previously described, with affinity constants spanning from micromolar to millimolar.
Foteini Karapanagioti, Sebastian Obermaier, Dirk J. Slotboom, Bert Poolman   +3 more
wiley   +1 more source

Attention based convolutional neural network for predicting RNA-protein binding sites [PDF]

NIPS 2017 Computational Biology Workshop, 2017
RNA-binding proteins (RBPs) play crucial roles in many biological processes, e.g. gene regulation. Computational identification of RBP binding sites on RNAs are urgently needed. In particular, RBPs bind to RNAs by recognizing sequence motifs. Thus, fast locating those motifs on RNA sequences is crucial and time-efficient for determining whether the ...
arxiv  

The cytoskeletal control of B cell receptor and integrin signaling in normal B cells and chronic lymphocytic leukemia

FEBS Letters, EarlyView.
In lymphoid organs, antigen recognition and B cell receptor signaling rely on integrins and the cytoskeleton. Integrins act as mechanoreceptors, couple B cell receptor activation to cytoskeletal remodeling, and support immune synapse formation as well as antigen extraction.
Abhishek Pethe, Tanja Nicole Hartmann
wiley   +1 more source

Measuring similarities between transcription factor binding sites

BMC Bioinformatics, 2005
Background Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profiles complicate large scale analysis of transcription factor binding sites ...
Gonze Didier, Kielbasa Szymon M, Herzel Hanspeter   +2 more
doaj   +1 more source

Unlocking the potential of tumor‐derived DNA in urine for cancer detection: methodological challenges and opportunities

Molecular Oncology, EarlyView.
Urine is a rich source of biomarkers for cancer detection. Tumor‐derived material is released into the bloodstream and transported to the urine. Urine can easily be collected from individuals, allowing non‐invasive cancer detection. This review discusses the rationale behind urine‐based cancer detection and its potential for cancer diagnostics ...
Birgit M. M. Wever, Renske D. M. Steenbergen   +1 more
wiley   +1 more source

Predicting protein-protein binding sites in membrane proteins

BMC Bioinformatics, 2009
Background Many integral membrane proteins, like their non-membrane counterparts, form either transient or permanent multi-subunit complexes in order to carry out their biochemical function.
Bordner Andrew J
doaj   +1 more source

Surfaceome: a new era in the discovery of immune evasion mechanisms of circulating tumor cells

Molecular Oncology, EarlyView.
In the era of immunotherapies, many patients either do not respond or eventually develop resistance. We propose to pave the way for proteomic analysis of surface‐expressed proteins called surfaceome, of circulating tumor cells. This approach seeks to identify immune evasion mechanisms and discover potential therapeutic targets. Circulating tumor cells (
Doryan Masmoudi, Jérome Vialaret, Christophe Hirtz, Catherine Alix‐Panabières   +3 more
wiley   +1 more source

QPS -- quadratic programming sampler, a motif finder using biophysical modeling [PDF]

arXiv, 2008
We present a Markov chain Monte Carlo algorithm for local alignments of nucleotide sequences aiming to infer putative transcription factor binding sites, referred to as the quadratic programming sampler. The new motif finder incorporates detailed biophysical modeling of the transcription factor binding site recognition which arises an intrinsic ...
arxiv  

Clinical applications of next‐generation sequencing‐based ctDNA analyses in breast cancer: defining treatment targets and dynamic changes during disease progression

Molecular Oncology, EarlyView.
Circulating tumor DNA (ctDNA) offers a possibility for different applications in early and late stage breast cancer management. In early breast cancer tumor informed approaches are increasingly used for detecting molecular residual disease (MRD) and early recurrence. In advanced stage, ctDNA provides a possibility for monitoring disease progression and
Eva Valentina Klocker, Samantha Hasenleithner, Rupert Bartsch, Simon P. Gampenrieder, Daniel Egle, Christian F. Singer, Gabriel Rinnerthaler, Michael Hubalek, Katja Schmitz, Zsuzsanna Bago‐Horvath, Andreas Petzer, Sonja Heibl, Ellen Heitzer, Marija Balic, Michael Gnant   +14 more
wiley   +1 more source