Protein quaternary structureProtein quaternary structure is the fourth (and highest) classification level of protein structure. Protein quaternary structure refers to the structure of proteins which are themselves composed of two or more smaller protein chains (also referred to as subunits). Protein quaternary structure describes the number and arrangement of multiple folded protein subunits in a multi-subunit complex. It includes organizations from simple dimers to large homooligomers and complexes with defined or variable numbers of subunits.
Nucleic acid structure predictionNucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. Secondary structure can be predicted from one or several nucleic acid sequences. Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known).
Feedforward neural networkA feedforward neural network (FNN) is one of the two broad types of artificial neural network, characterized by direction of the flow of information between its layers. Its flow is uni-directional, meaning that the information in the model flows in only one direction—forward—from the input nodes, through the hidden nodes (if any) and to the output nodes, without any cycles or loops, in contrast to recurrent neural networks, which have a bi-directional flow.
Disjoint union of graphsIn graph theory, a branch of mathematics, the disjoint union of graphs is an operation that combines two or more graphs to form a larger graph. It is analogous to the disjoint union of sets, and is constructed by making the vertex set of the result be the disjoint union of the vertex sets of the given graphs, and by making the edge set of the result be the disjoint union of the edge sets of the given graphs. Any disjoint union of two or more nonempty graphs is necessarily disconnected.
Sequence alignmentIn bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
Nucleic acid sequenceA nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the nucleotides. By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, with its double helix, there are two possible directions for the notated sequence; of these two, the sense strand is used.
Bipartite graphIn the mathematical field of graph theory, a bipartite graph (or bigraph) is a graph whose vertices can be divided into two disjoint and independent sets and , that is, every edge connects a vertex in to one in . Vertex sets and are usually called the parts of the graph. Equivalently, a bipartite graph is a graph that does not contain any odd-length cycles. The two sets and may be thought of as a coloring of the graph with two colors: if one colors all nodes in blue, and all nodes in red, each edge has endpoints of differing colors, as is required in the graph coloring problem.
Artificial neural networkArtificial neural networks (ANNs, also shortened to neural networks (NNs) or neural nets) are a branch of machine learning models that are built using principles of neuronal organization discovered by connectionism in the biological neural networks constituting animal brains. An ANN is based on a collection of connected units or nodes called artificial neurons, which loosely model the neurons in a biological brain. Each connection, like the synapses in a biological brain, can transmit a signal to other neurons.
Symmetric graphIn the mathematical field of graph theory, a graph G is symmetric (or arc-transitive) if, given any two pairs of adjacent vertices u_1—v_1 and u_2—v_2 of G, there is an automorphism such that and In other words, a graph is symmetric if its automorphism group acts transitively on ordered pairs of adjacent vertices (that is, upon edges considered as having a direction). Such a graph is sometimes also called 1-arc-transitive or flag-transitive. By definition (ignoring u_1 and u_2), a symmetric graph without isolated vertices must also be vertex-transitive.
Eulerian pathIn graph theory, an Eulerian trail (or Eulerian path) is a trail in a finite graph that visits every edge exactly once (allowing for revisiting vertices). Similarly, an Eulerian circuit or Eulerian cycle is an Eulerian trail that starts and ends on the same vertex. They were first discussed by Leonhard Euler while solving the famous Seven Bridges of Königsberg problem in 1736. The problem can be stated mathematically like this: Given the graph in the image, is it possible to construct a path (or a cycle; i.
