Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for in silico analyses of biological queries using computational and statistical techniques.
In computer science, the computational complexity or simply complexity of an algorithm is the amount of resources required to run it. Particular focus is given to computation time and memory storage requirements. The complexity of a problem is the complexity of the best algorithms that allow solving the problem.
In theoretical computer science and mathematics, computational complexity theory focuses on classifying computational problems according to their resource usage, and relating these classes to each other. A computational problem is a task solved by a computer. A computation problem is solvable by mechanical application of mathematical steps, such as an algorithm.
In theoretical computer science and mathematics, the theory of computation is the branch that deals with what problems can be solved on a model of computation, using an algorithm, how efficiently they can be solved or to what degree. The field is divided into three major branches: automata theory and formal languages, computability theory, and computational complexity theory, which are linked by the question: "What are the fundamental capabilities and limitations of computers?".
In the mathematical field of graph theory the Hamiltonian path problem and the Hamiltonian cycle problem are problems of determining whether a Hamiltonian path or a Hamiltonian cycle exists in a given graph. Both problems are NP-complete.
DNA computing is an emerging branch of unconventional computing which uses DNA, biochemistry, and molecular biology hardware, instead of the traditional electronic computing. Research and development in this area concerns theory, experiments, and applications of DNA computing. Although the field originally started with the demonstration of a computing application by Len Adleman in 1994, it has now been expanded to several other avenues such as the development of storage technologies, nanoscale imaging modalities, synthetic controllers and reaction networks, etc.
Theoretical computer science (TCS) is a subset of general computer science and mathematics that focuses on mathematical aspects of computer science such as the theory of computation, lambda calculus, and type theory.
Structural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models. The term structural has the same meaning as in structural biology, and structural bioinformatics can be seen as a part of computational structural biology. The main objective of structural bioinformatics is the creation of new methods of analysing and manipulating biological macromolecular data in order to solve problems in biology and generate new knowledge.
Pancake sorting is the mathematical problem of sorting a disordered stack of pancakes in order of size when a spatula can be inserted at any point in the stack and used to flip all pancakes above it. A pancake number is the minimum number of flips required for a given number of pancakes. In this form, the problem was first discussed by American geometer Jacob E. Goodman. A variant of the problem is concerned with burnt pancakes, where each pancake has a burnt side and all pancakes must, in addition, end up with the burnt side on bottom.
In the mathematical area of graph theory, a clique is a subset of vertices of an undirected graph such that every two distinct vertices in the clique are adjacent. That is, a clique of a graph is an induced subgraph of that is complete. Cliques are one of the basic concepts of graph theory and are used in many other mathematical problems and constructions on graphs. Cliques have also been studied in computer science: the task of finding whether there is a clique of a given size in a graph is NP-complete, but despite this hardness result, many algorithms for finding cliques have been studied.
In computational complexity theory, the Cook–Levin theorem, also known as Cook's theorem, states that the Boolean satisfiability problem is NP-complete. That is, it is in NP, and any problem in NP can be reduced in polynomial time by a deterministic Turing machine to the Boolean satisfiability problem.
In computational complexity theory, L is the complexity class containing decision problems that can be solved by a deterministic Turing machine using a logarithmic amount of writable memory space. Formally, the Turing machine has two tapes, one of which encodes the input and can only be read, whereas the other tape has logarithmic size but can be read as well as written. Logarithmic space is sufficient to hold a constant number of pointers into the input and a logarithmic number of boolean flags, and many basic logspace algorithms use the memory in this way.
Protein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein function. Proteins can be designed from scratch or by making calculated variants of a known protein structure and its sequence. Rational protein design approaches make protein-sequence predictions that will fold to specific structures. These predicted sequences can then be validated experimentally through methods such as peptide synthesis, site-directed mutagenesis, or artificial gene synthesis.
In artificial intelligence, artificial immune systems (AIS) are a class of computationally intelligent, rule-based machine learning systems inspired by the principles and processes of the vertebrate immune system. The algorithms are typically modeled after the immune system's characteristics of learning and memory for use in problem-solving.
Unconventional computing is computing by any of a wide range of new or unusual methods. It is also known as alternative computing.
Biological computers use biologically derived molecules — such as DNA and/or proteins — to perform digital or real computations.
Lateral computing is a lateral thinking approach to solving computing problems. Lateral thinking has been made popular by Edward de Bono. This thinking technique is applied to generate creative ideas and solve problems. Similarly, by applying lateral-computing techniques to a problem, it can become much easier to arrive at a computationally inexpensive, easy to implement, efficient, innovative or unconventional solution.
Natural computing, also called natural computation, is a terminology introduced to encompass three classes of methods: 1) those that take inspiration from nature for the development of novel problem-solving techniques; 2) those that are based on the use of computers to synthesize natural phenomena; and 3) those that employ natural materials to compute. The main fields of research that compose these three branches are artificial neural networks, evolutionary algorithms, swarm intelligence, artificial immune systems, fractal geometry, artificial life, DNA computing, and quantum computing, among others.
Molecular Operating Environment (MOE) is a drug discovery software platform that integrates visualization, modeling and simulations, as well as methodology development, in one package. MOE scientific applications are used by biologists, medicinal chemists and computational chemists in pharmaceutical, biotechnology and academic research. MOE runs on Windows, Linux, Unix, and macOS. Main application areas in MOE include structure-based design, fragment-based design, ligand-based design, pharmacophore discovery, medicinal chemistry applications, biologics applications, structural biology and bioinformatics, protein and antibody modeling, molecular modeling and simulations, virtual screening, cheminformatics & QSAR. The Scientific Vector Language (SVL) is the built-in command, scripting and application development language of MOE.
