Related papers: Three dimensional chaos game representation of pro…
We review the occurrence of the patterns of the onset of chaos in low-dimensional nonlinear dissipative systems in leading topics of condensed matter physics and complex systems of various disciplines. We consider the dynamics associated…
The network paradigm is increasingly used to describe the dynamics of complex systems. Here we review the current results and propose future development areas in the assessment of perturbation waves, i.e. propagating structural changes in…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
Chaos presents complex dynamics arising from nonlinearity and a sensitivity to initial states. These characteristics suggest a depth of expressivity that underscores their potential for advanced computational applications. However,…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
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…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
The distance-geometric graph representation adopts a unified scheme (distance) for representing the geometry of three-dimensional(3D) graphs. It is invariant to rotation and translation of the graph and it reflects pair-wise node…
We consider representation learning for proteins with 3D structures. We build 3D graphs based on protein structures and develop graph networks to learn their representations. Depending on the levels of details that we wish to capture,…
Extensively exploring protein conformational landscapes remains a major challenge in computational biology due to the high computational cost involved in dynamic physics-based simulations. In this work, we propose a novel pipeline, MoDyGAN,…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
This paper presents a new method for 3D action recognition with skeleton sequences (i.e., 3D trajectories of human skeleton joints). The proposed method first transforms each skeleton sequence into three clips each consisting of several…
Protein language models often take into consideration the alignment between a protein sequence and its textual description. However, they do not take structural information into consideration. Traditional methods treat sequence and…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
Graph theory and graph mining constitute rich fields of computational techniques to study the structures, topologies and properties of graphs. These techniques constitute a good asset in bioinformatics if there exist efficient methods for…
Protein complexes are macromolecules essential to the functioning and well-being of all living organisms. As the structure of a protein complex, in particular its region of interaction between multiple protein subunits (i.e., chains), has a…
In this study, we tackle the challenging task of predicting secondary structures from protein primary sequences, a pivotal initial stride towards predicting tertiary structures, while yielding crucial insights into protein activity,…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…