Protein dynamics, thermal stability, and free-energy landscapes: A molecular dynamics investigation
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Proteins' biological functions are defined by the geometric and chemical structure of their 3D molecular surfaces. Recent works have shown that geometric deep learning can be used on mesh-based representations of proteins to identify potential functional s ...
Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. We present RADI/raDIMod, a variation of the original DCA algorithm that grou ...
The present relates to a method for generating variants of a protein based on a native protein regulated by allosteric pathway, the method comprising: - i) providing 3D structures of the native protein; - ii) identifying at least one pair of coupled allost ...
Limb amputation is characterized by complex and intermingled brain reorganization processes combining sensorimotor deprivation induced by the loss of the limb per se, and compensatory behaviors, such as the over-use of the intact or remaining limb. While a ...
Continuous assessment of transferable forcefields for molecular simulations is essential to identify their weaknesses and direct improvement efforts. The latest efforts focused on better describing disordered proteins while retaining proper description of ...
The functionality of proteins is governed by the interplay between their structure and dynamics. Thus, understanding the mechanism and nature of protein motion is essential to understand their biological activity. Here we present and evaluate a novel metho ...
Imaging of proteins at the single-molecule level can reveal conformational variability, which is essential for the understanding of biomolecules. To this end, a biologically relevant state of the sample must be retained during both sample preparation and i ...
The present relates to a method for generating variants of a protein based on a native protein regulated by allosteric pathway, the method comprising:- i) providing 3D structures of the native protein;- ii) identifying at least one pair of coupled alloster ...
We present an open-source program irvsp, to compute irreducible representations of electronic states for all 230 space groups with an interface to the Vienna ab-initio Simulation Package. This code is fed with plane-wave-based wavefunctions (e.g. WAVECAR) ...
Characters do not convey meaning, but sequences of characters do. We propose an unsupervised distributional method to learn the abstract meaning-bearing units in a sequence of characters. Rather than segmenting the sequence, this model discovers continuous ...