Implicit solvationImplicit solvation (sometimes termed continuum solvation) is a method to represent solvent as a continuous medium instead of individual “explicit” solvent molecules, most often used in molecular dynamics simulations and in other applications of molecular mechanics. The method is often applied to estimate free energy of solute-solvent interactions in structural and chemical processes, such as folding or conformational transitions of proteins, DNA, RNA, and polysaccharides, association of biological macromolecules with ligands, or transport of drugs across biological membranes.
Protein foldingProtein folding is the physical process where a protein chain is translated into its native three-dimensional structure, typically a "folded" conformation, by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA into a linear chain of amino acids.
KnowledgeKnowledge is a form of awareness or familiarity. It is often understood as awareness of facts or as practical skills, and may also mean familiarity with objects or situations. Knowledge of facts, also called propositional knowledge, is often defined as true belief that is distinct from opinion or guesswork by virtue of justification. While there is wide agreement among philosophers that propositional knowledge is a form of true belief, many controversies in philosophy focus on justification.
ProteinProteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.
Declarative knowledgeDeclarative knowledge is an awareness of facts that can be expressed using declarative sentences, like knowing that Princess Diana died in 1997. It is also called theoretical knowledge, descriptive knowledge, propositional knowledge, and knowledge-that. It is not restricted to one specific use or purpose and can be stored in books or on computers. Epistemology is the main discipline studying declarative knowledge. Among other things, it studies the essential components of declarative knowledge.
Knowledge managementKnowledge management (KM) is the collection of methods relating to creating, sharing, using and managing the knowledge and information of an organization. It refers to a multidisciplinary approach to achieve organizational objectives by making the best use of knowledge. An established discipline since 1991, KM includes courses taught in the fields of business administration, information systems, management, library, and information science. Other fields may contribute to KM research, including information and media, computer science, public health and public policy.
Drug designDrug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that activates or inhibits the function of a biomolecule such as a protein, which in turn results in a therapeutic benefit to the patient. In the most basic sense, drug design involves the design of molecules that are complementary in shape and charge to the biomolecular target with which they interact and therefore will bind to it.
Knowledge economyThe knowledge economy, or knowledge-based economy, is an economic system in which the production of goods and services is based principally on knowledge-intensive activities that contribute to advancement in technical and scientific innovation. The key element of value is the greater dependence on human capital and intellectual property as the source of innovative ideas, information and practices. Organisations are required to capitalise on this "knowledge" in their production to stimulate and deepen the business development process.
Knowledge sharingKnowledge sharing is an activity through which knowledge (namely, information, skills, or expertise) is exchanged among people, friends, peers, families, communities (for example, Wikipedia), or within or between organizations. It bridges the individual and organizational knowledge, improving the absorptive and innovation capacity and thus leading to sustained competitive advantage of companies as well as individuals. Knowledge sharing is part of the knowledge management process.
Protein designProtein 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 (de novo design) or by making calculated variants of a known protein structure and its sequence (termed protein redesign). Rational protein design approaches make protein-sequence predictions that will fold to specific structures.
Definitions of knowledgeDefinitions of knowledge try to determine the essential features of knowledge. Closely related terms are conception of knowledge, theory of knowledge, and analysis of knowledge. Some general features of knowledge are widely accepted among philosophers, for example, that it constitutes a cognitive success or an epistemic contact with reality and that propositional knowledge involves true belief. Most definitions of knowledge in analytic philosophy focus on propositional knowledge or knowledge-that, as in knowing that Dave is at home, in contrast to knowledge-how (know-how) expressing practical competence.
DesignA design is a concept of either an object, a process, or a system that is specific and, in most cases, detailed. Design refers to something that is or has been intentionally created by a thinking agent, though it is sometimes used to refer to the nature of something. The verb to design expresses the process of developing a design. In some cases, the direct construction of an object without an explicit prior plan may also be considered to be a design (such as in some artwork and craftwork).
Knowledge marketA knowledge market is a mechanism for distributing knowledge resources. There are two views on knowledge and how knowledge markets can function. One view uses a legal construct of intellectual property to make knowledge a typical scarce resource, so the traditional commodity market mechanism can be applied directly to distribute it. An alternative model is based on treating knowledge as a public good and hence encouraging free sharing of knowledge. This is often referred to as attention economy.
Procedural knowledgeProcedural knowledge (also known as knowing-how, and sometimes referred to as practical knowledge, imperative knowledge, or performative knowledge) is the knowledge exercised in the performance of some task. Unlike descriptive knowledge (also known as declarative knowledge, propositional knowledge or "knowing-that"), which involves knowledge of specific facts or propositions (e.g. "I know that snow is white"), procedural knowledge involves one's ability to do something (e.g. "I know how to change a flat tire").
Protein fold classIn molecular biology, protein fold classes are broad categories of protein tertiary structure topology. They describe groups of proteins that share similar amino acid and secondary structure proportions. Each class contains multiple, independent protein superfamilies (i.e. are not necessarily evolutionarily related to one another). Four large classes of protein that are generally agreed upon by the two main structure classification databases (SCOP and CATH).
Knowledge transferKnowledge transfer is the sharing or disseminating of knowledge and the providing of inputs to problem solving. In organizational theory, knowledge transfer is the practical problem of transferring knowledge from one part of the organization to another. Like knowledge management, knowledge transfer seeks to organize, create, capture or distribute knowledge and ensure its availability for future users. It is considered to be more than just a communication problem.
Fusion proteinFusion proteins or chimeric (kī-ˈmir-ik) proteins (literally, made of parts from different sources) are proteins created through the joining of two or more genes that originally coded for separate proteins. Translation of this fusion gene results in a single or multiple polypeptides with functional properties derived from each of the original proteins. Recombinant fusion proteins are created artificially by recombinant DNA technology for use in biological research or therapeutics.
Water modelIn computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called site, (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects.
DrugA drug is any chemical substance that causes a change in an organism's physiology or psychology when consumed. Drugs are typically distinguished from food and substances that provide nutritional support. Consumption of drugs can be via inhalation, injection, smoking, ingestion, absorption via a patch on the skin, suppository, or dissolution under the tongue. In pharmacology, a drug is a chemical substance, typically of known structure, which, when administered to a living organism, produces a biological effect.
Protein–protein interactionProtein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context. Proteins rarely act alone as their functions tend to be regulated.
