Related papers: Binding-and-folding recognition of an intrinsicall…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a…
Inverse protein folding is challenging due to its inherent one-to-many mapping characteristic, where numerous possible amino acid sequences can fold into a single, identical protein backbone. This task involves not only identifying viable…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
Protein folding is an indispensable process for the majority of proteins after their synthesis from ribosomes in the cell. Most in vitro protein folding studies have focused on single-domain proteins. Hence, it is important to understand…
The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the Literature, although the number of statistically significant structural studies supporting this is surprisingly low. At variance with…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
Proteins perform a large variety of functions in living organisms, thus playing a key role in biology. As of now, available learning algorithms to process protein data do not consider several particularities of such data and/or do not scale…
The recent breakthrough of AlphaFold3 in modeling complex biomolecular interactions, including those between proteins and ligands, nucleotides, or metal ions, creates new opportunities for protein design. In so-called inverse protein…
In this paper, we present a strategy for training convolutional neural networks to effectively resolve interference arising from competing hypotheses relating to inter-categorical information throughout the network. The premise is based on…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Prediction of protein-ligand complexes for flexible proteins remains still a challenging problem in computational structural biology and drug design. Here we present two novel deep neural network approaches with significant improvement in…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
Recent demonstrations of extraordinary stabilization of proteins in mobile protic [1] and aprotic [2] ionic liquid solutions at ambient temperatures have raised hopes of new biopreservation and drug transportation technologies. Here we…