Related papers: Sensitivity of protein rigidity analysis to small …
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
This paper was motivated by the articles "Same or different - that is the question" in CrystEngComm (July 2020) and "Change to the definition of a crystal" in the IUCr newsletter (June 2021). Experimental approaches to crystal comparisons…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
Discerning how a mutation affects the stability of a protein is central to the study of a wide range of diseases. Machine learning and statistical analysis techniques can inform how to allocate limited resources to the considerable time and…
This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
In the context of complex systems and, particularly, of protein folding, a physically meaningful distance is defined which allows to make useful statistical statements about the way in which energy differences are modified when two…
This paper investigates a well-posedness property of parametric constraint systems named here Robinson stability. Based on advanced tools of variational analysis and generalized differentiation, we derive first-order and second-order…
The paper presents a new stiffness modelling method for multi-chain parallel robotic manipulators with flexible links and compliant actuating joints. In contrast to other works, the method involves a FEA-based link stiffness evaluation and…
For the contact of two finite portions of interacting rigid crystalline surfaces, we compute the dependence of the pinning energy barrier on the misfit angle and contact area. The resulting data are used to investigate the distribution of…
Woven shell structures are beneficial for applications requiring lightweight, damage resilience, and design tunability, such as in wearable devices, soft robotics, and aerospace systems. A fundamental component of woven structures is the…
The widespread application of machine learning (ML) to the chemical sciences is making it very important to understand how the ML models learn to correlate chemical structures with their properties, and what can be done to improve the…
We present a survey of results concerning the use of inductive constructions to study the rigidity of frameworks. By inductive constructions we mean simple graph moves which can be shown to preserve the rigidity of the corresponding…
Graph similarity search algorithms usually leverage the structural properties of a database. Hence, these algorithms are effective only on some structural variations of the data and are ineffective on other forms, which makes them hard to…
An analytical model based on variational principles for a thin-walled stiffened plate subjected to axial compression is presented. A system of nonlinear differential and integral equations is derived and solved using numerical continuation.…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
In a recent work we proposed a coarse-grained methodology for studying the response of peptides when simulated at different values of pH; in this work we extend the methodology to analyze the pH-dependent behavior of coiled coils. This…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…