Related papers: Flexibility-Rigidity Index for Protein-Nucleic Aci…

We present a computational framework for analyzing and quantifying system flexibility. Our framework incorporates new features that include: general uncertainty characterizations that are constructed using composition of sets, procedures…

Proteins are essential biological macromolecules that execute life functions. Local structural motifs, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution…

Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…

Neural networks commonly execute on hardware accelerators such as NPUs and GPUs for their size and computation overhead. These accelerators are costly and it is hard to scale their resources to handle real-time workload fluctuations. We…

It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…

Rigidity analysis using the "pebble game" has been applied to protein crystal structures to obtain information on protein folding, assembly and t he structure-function relationship. However, previous work using this technique has not made…

Internal coordinate molecular dynamics (ICMD) is an efficient method for studying biopolymers, but it is readily applicable only to molecules with tree topologies, that is with no internal flexible rings. Common examples violating this…

This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…

Structural assessment of biomolecular complexes is vital for translating molecular models into functional insights, shaping our understanding of biology and aiding drug discovery. However, current structure-based scoring functions often…

The interaction between proteins and nucleic acids is crucial for processes that sustain cellular function, including DNA maintenance and the regulation of gene expression and translation. Amino acid mutations in protein-nucleic acid…

Statistical techniques are needed to analyse data structures with complex dependencies such that clinically useful information can be extracted. Individual-specific networks, which capture dependencies in complex biological systems, are…

Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…

Ultrasound-based elasticity imaging is a non-invasive technique for estimating tissue stiffness fields from displacement fields obtained by comparing ultrasound signals before and after compression. While recent deep learning approaches…

Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…

The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…

Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…

Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation…

Protein flexibility is crucial for understanding protein structures, functions, and dynamics, and it can be measured through experimental methods such as X-ray crystallography. Theoretical approaches have also been developed to predict…

Gaussian network model (GNM) is one of the most accurate and efficient methods for biomolecular flexibility analysis. However, the systematic generalization of the GNM has been elusive. We show that the GNM Kirchhoff matrix can be built…

Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure,…