Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

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Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

The tip of the red giant branch (TRGB) is an important standard candle for determining luminosity distances. Although several 105 small-amplitude red giant stars (SARGs) have been discovered, variability was previously considered irrelevant for the TRGB as ...

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Upcoming wide-field surveys will discover thousands of new strongly lensed quasars which will be monitored with unprecedented cadence by the Legacy Survey of Space and Time (LSST). Many of these quasars will undergo caustic-crossing events over the 10-yr L ...

This study combined protein modeling methods to generate the prolamins' fractions as precise as possible. Hence, gliadins, zeins, kafirins, hordeins, secalins, avenins and oryzins were generated based on their characteristics and disulfide mapping. Finding ...

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

As large, data-driven artificial intelligence models become ubiquitous, guaranteeing high data quality is imperative for constructing models. Crowdsourcing, community sensing, and data filtering have long been the standard approaches to guaranteeing or imp ...

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

Microsecond time-resolved cryo-electron microscopy has emerged as a novel approach for directly observing protein dynamics. By providing microsecond temporal and near-atomic spatial resolution, it has the potential to elucidate a wide range of dynamics tha ...

Data-driven approaches have been applied to reduce the cost of accurate computational studies on materials, by using only a small number of expensive reference electronic structure calculations for a representative subset of the materials space, and using ...

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learni ...

Electrical stimulation of the nervous system has emerged as a promising assistive technology in case of many injuries and illnesses across various parts of the nervous system. In particular, the invasive neuromodulation of the peripheral nervous system see ...

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

We construct a measure on the thick points of a Brownian loop soup in a bounded domain D

D

of the plane with given intensity theta>0

\theta >0

, which is formally obtained by exponentiating the square root of its occupation field. The measure is construct ...

Time has always been a central factor in understanding the challenges of daily mobility. For a long time, and still today, methods of economic evaluation of transport projects have monetized time savings so that they can be included in the cost–benefit ana ...

The beta spectrum of the main transition of the 171Tm was measured using a double focalizing spectrometer. The instrument was lately improved in order to reduce its low energy threshold to 34 keV. We used the spectrometer to measure the energy end-point of ...

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the su ...

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

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Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Predicting protein interactions using geometric deep learning on protein surfaces

Small-amplitude Red Giants Elucidate the Nature of the Tip of the Red Giant Branch as a Standard Candle

Opportunities and challenges in design and optimization of protein function

Resolving the vicinity of supermassive black holes with gravitational microlensing

Prolamins' 3D structure: A new insight into protein modeling using the language of numbers and shapes

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Microsecond Time-Resolved Cryo-Electron Microscopy

Extensions of Peer Prediction Incentive Mechanisms

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Microsecond time-resolved cryo-electron microscopy

Efficient and insightful descriptors for representing molecular and material space

Computational drug development for membrane protein targets

Biophysically accurate and machine learning-based surrogate models to optimize neuroprosthesis design and operation

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Multiplicative chaos of the Brownian loop soup

Appropriations and Uses of Travel Time

Measurement of the 171Tm beta spectrum

Protein target highlights in CASP15: Analysis of models by structure providers