Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states
E Brunk, U Rothlisberger - Chemical reviews, 2015 - ACS Publications
The quantum nature of electrons and nuclei is manifested in countless biological events
including the rearrangements of electrons in biochemical reactions, electron and proton …
including the rearrangements of electrons in biochemical reactions, electron and proton …
Modeling protein association mechanisms and kinetics
Highlights•Protein association rate constants are essential for cellular functions.•Half of the
problem of modeling association kinetics has a solution.•Binding of disordered proteins …
problem of modeling association kinetics has a solution.•Binding of disordered proteins …
Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity
The spike (S) glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-
2) is responsible for the binding to the permissive cells. The receptor-binding domain (RBD) …
2) is responsible for the binding to the permissive cells. The receptor-binding domain (RBD) …
Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli
Genome-scale network reconstruction has enabled predictive modeling of metabolism for
many systems. Traditionally, protein structural information has not been represented in such …
many systems. Traditionally, protein structural information has not been represented in such …
Systems biology of the structural proteome
Background The success of genome-scale models (GEMs) can be attributed to the high-
quality, bottom-up reconstructions of metabolic, protein synthesis, and transcriptional …
quality, bottom-up reconstructions of metabolic, protein synthesis, and transcriptional …
Towards structural systems pharmacology to study complex diseases and personalized medicine
Genome-Wide Association Studies (GWAS), whole genome sequencing, and high-
throughput omics techniques have generated vast amounts of genotypic and molecular …
throughput omics techniques have generated vast amounts of genotypic and molecular …
Understanding large scale sequencing datasets through changes to protein folding
D Shorthouse, H Lister, GS Freeman… - Briefings in Functional …, 2024 - academic.oup.com
The expansion of high-quality, low-cost sequencing has created an enormous opportunity to
understand how genetic variants alter cellular behaviour in disease. The high diversity of …
understand how genetic variants alter cellular behaviour in disease. The high diversity of …
Structural systems pharmacology: the role of 3D structures in next-generation drug development
Structural systems pharmacology offers a novel way of approaching drug discovery by
considering the global physiological environment of protein targets, and the effects derived …
considering the global physiological environment of protein targets, and the effects derived …
Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma
As malignant transformation requires synchronization of growth-driving signaling (S) and
metabolic (M) pathways, defining cancer-specific SM interconnected networks (SMINs) …
metabolic (M) pathways, defining cancer-specific SM interconnected networks (SMINs) …
Structural prediction of protein–protein interactions by docking: Application to biomedical problems
D Barradas-Bautista, M Rosell, C Pallara… - Advances in protein …, 2018 - Elsevier
A huge amount of genetic information is available thanks to the recent advances in
sequencing technologies and the larger computational capabilities, but the interpretation of …
sequencing technologies and the larger computational capabilities, but the interpretation of …