Related papers: The eBDIMS path-sampling server: generation, class…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
With the exponential increase of the protein sequence databases over time, multiple-sequence alignment (MSA) methods, like PSI-BLAST, perform exhaustive and time-consuming database search to retrieve evolutionary information. The resulting…
We present a software tool -- extended Dynamic Causal Modelling for Phase Coupling (eDCM PC) -- that is able to estimate effective connectivity between any kind of oscillating systems, e.g. distant brain regions, using the phase information…
Cryo-electron tomography (cryo-ET) has emerged as a powerful tool for studying the structural heterogeneity of proteins and their complexes, offering insights into macromolecular dynamics directly within cells. Driven by recent…
Using random walk sampling methods for feature learning on networks, we develop a method for generating low-dimensional node embeddings for directed graphs and identifying transition states of stochastic chemical reacting systems. We…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
Background and Objective: Hemodynamic analysis of blood flow through arteries and veins is critical for diagnosing cardiovascular diseases, such as aneurysms and stenoses, and for investigating cardiovascular parameters, such as turbulence…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
Much scientific enquiry across disciplines is founded upon a mechanistic treatment of dynamic systems that ties form to function. A highly visible instance of this is in molecular biology, where an important goal is to determine…
Convolutional Neural Network (CNN)-based machine learning systems have made breakthroughs in feature extraction and image recognition tasks in two dimensions (2D). Although there is significant ongoing work to apply CNN technology to…
Protein subcellular localization is an important factor in normal cellular processes and disease. While many protein localization resources treat it as static, protein localization is dynamic and heavily influenced by biological context.…
We present an unsupervised data processing workflow that is specifically designed to obtain a fast conformational clustering of long molecular dynamics simulation trajectories. In this approach we combine two dimensionality reduction…
The identification of bitter peptides is crucial in various domains, including food science, drug discovery, and biochemical research. These peptides not only contribute to the undesirable taste of hydrolyzed proteins but also play key…
Contemporary materials science research is heavily conducted in silico, involving massive simulations of the atomic-scale evolution of materials. Cataloging basic patterns in the atomic displacements is key to understanding and predicting…
In this work we present a novel, robust transition generation technique that can serve as a new tool for 3D animators, based on adversarial recurrent neural networks. The system synthesizes high-quality motions that use temporally-sparse…
Cryo-electron microscopy (cryo-EM) has revolutionized experimental protein structure determination. Despite advances in high resolution reconstruction, a majority of cryo-EM experiments provide either a single state of the studied…
Continuum or hybrid modeling of bilayer membrane morphological dynamics induced by embedded proteins necessitates the identification of protein-membrane interfaces and coupling of deformations of two surfaces. In this article we developed…
We performed "weighted ensemble" path-sampling simulations of adenylate kinase, using several semi-atomistic protein models. Our study investigated both the biophysics of conformational transitions as well as the possibility of increasing…
Modeling deformable objects - especially continuum materials - in a way that is physically plausible, generalizable, and data-efficient remains challenging across 3D vision, graphics, and robotic manipulation. Many existing methods…