Related papers: Finding Multiple Reaction Pathways of Ligand Unbin…
Cells use surface receptors to estimate the concentration of external ligands. Limits on the accuracy of such estimations have been well studied for pairs of ligand and receptor species. However, the environment typically contains many…
We proposed a new technique to accelerate sampling methods for solving difficult optimization problems. Our method investigates the intrinsic connection between posterior distribution sampling and optimization with Langevin dynamics, and…
Prediction of ligand binding sites of proteins is a fundamental and important task for understanding the function of proteins and screening potential drugs. Most existing methods require experimentally determined protein holo-structures as…
Deep neural networks have achieved state of the art accuracy at classifying molecules with respect to whether they bind to specific protein targets. A key breakthrough would occur if these models could reveal the fragment pharmacophores…
The development of signal unmixing algorithms is essential for leveraging multimodal datasets acquired through a wide array of scientific imaging technologies, including hyperspectral or time-resolved acquisitions. In experimental physics,…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…
This paper develops the concept of decomposition for chemical reaction networks, based on which a network decomposition technique is proposed to capture the stability of large-scale networks characterized by a high number of species, high…
Ring-polymer molecular dynamics (RPMD) has become a popular method for describing chemical reactions due to its ability to simultaneously capture tunneling, zero-point energy, anharmonicity and recrossing. Here we highlight that despite its…
As computational chemistry methods evolve, dynamic effects have been increasingly recognized to govern chemical reaction pathways in both organic and inorganic systems. Here, we introduce a committor-based workflow that integrates a…
Genes/Proteins do not work alone within our body, rather as a group they perform certain activities indicated as pathways. Signalling transduction pathways (STPs) are some of the important pathways that transmit biological signals from…
The utilization of multiple phosphorylation sites in regulating a biological response is ubiquitous in cell signaling. If each site contributes an additional, equivalent binding site, then one consequence of an increase in the number of…
Spatio-temporal biochemical signaling in a large class of protein-protein interaction networks is well modeled by a reaction-diffusion system. The global existence of the solution to the reaction-diffusion system is determined by the…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
A method to approximate transmission probabilities for a nonseparable multidimensional barrier is applied to a waveguide model. The method uses complex barrier-crossing orbits to represent reaction probabilities in phase space and is…
The dissociation of ligands from proteins and other biomacromolecules occurs over a wide range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far beyond those that are accessible by conventional molecular…
In this paper, we show that unbalanced optimal transport provides a convenient framework to handle reaction and diffusion processes in a unified metric framework. We use a constructive method, alternating minimizing movements for the…
Retinoic acid receptor (RAR) is a ligand-dependent transcription factor that regulates the expression of genes involved in cell growth, differentiation, and development. Binding of the retinoic acid hormone to RAR is accompanied by…
Understanding anomalous transport and reaction kinetics due to microscopic physical and chemical disorder is a long-standing goal in many fields including geophysics, biology, and engineering. We consider reaction-diffusion characterized by…
We present a theory of unbinding transitions for membranes that interact via short and long receptor/ligand bonds. The detail of unbinding behavior of the membranes is governed by the binding energies and concentrations of receptors and…
In this paper, we propose a new method to identify biochemical reaction networks (i.e. both reactions and kinetic parameters) from heterogeneous datasets. Such datasets can contain (a) data from several replicates of an experiment performed…