The Institute of Neurophysiopathology (INP) welcomes tenured researchers/lecturers, and junior researchers seeking a permanent position in France to lead or strengthen its research programs RESEARCHER...

PhD Project - EastBio - Identification of target genes for control of economically important plant pathogens using large foundation models (LFMs) at The James Hutton Institute, listed on FindAPhD.com

ALT: a man is standing in front of a sphere with the words science written on it .

Machine learning has become ubiquitous in materials modelling and now routinely enables large-scale atomistic simulations with quantum-mechanical accuracy. However, developing machine-learned interato...

The program provides up to $1.5 million in support for early career scientists across up to eight years, spanning postdoctoral training through the transition to starting a lab as faculty.

Quiescence in Saccharomyces cerevisiae is a reversible G0 crucial for long-term survival under nutrient-deprived conditions. During quiescence, the genome is hypoacetylated and chromatin undergoes sig...

Human RAD52 is a prime target for synthetical lethality approaches to treat cancers with deficiency in homologous recombination. Among multiple cellular roles of RAD52, its functions in homologous rec...

ALT: a cartoon drawing of a banana with arms and legs waving

Homologous recombination (HR) repairs double-stranded DNA breaks (DSBs). The DSBs are resected to yield single-stranded DNA (ssDNA) that are coated by Replication Protein A (RPA). Rad51 is a recombina...

Single-stranded DNA annealing is driven by RAD52 open rings in association with RPA.

We present the NetSci program–an open-source scientific software package designed for estimating mutual information (MI) between data sets using GPU acceleration and a k-nearest-neighbor algorithm. This approach significantly enhances calculation speed, achieving improvements of several orders of magnitude over traditional CPU-based methods, with data set size limits dictated only by available hardware. To validate NetSci, we accurately compute MI for an analytically verifiable two-dimensional Gaussian distribution and replicate the generalized correlation (GC) analysis previously conducted on the B1 domain of protein G. We also apply NetSci to molecular dynamics simulations of the Sarcoendoplasmic Reticulum Calcium-ATPase (SERCA) pump, exploring the allosteric mechanisms and pathways influenced by ATP and 2′-deoxy-ATP (dATP) binding. Our analysis reveals distinct allosteric effects induced by ATP compared to dATP, with predicted information pathways from the bound nucleotide to the calcium-binding domain differing based on the nucleotide involved. NetSci proves to be a valuable tool for estimating MI and GC in various data sets and is particularly effective for analyzing intraprotein communication and information transfer.

Protein design has focused primarily on the design of ground states, ensuring they are sufficiently low energy to be highly populated. Designing the kinetics and dynamics of a system requires, in addi...