Protein function predictionProtein function prediction methods are techniques that bioinformatics researchers use to assign biological or biochemical roles to proteins. These proteins are usually ones that are poorly studied or predicted based on genomic sequence data. These predictions are often driven by data-intensive computational procedures. Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of publications, phylogenetic profiles, phenotypic profiles, and protein-protein interaction.
Gene predictionIn computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced. In its earliest days, "gene finding" was based on painstaking experimentation on living cells and organisms.
Protein structure predictionProtein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; and it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes).
Protein–protein interaction predictionProtein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions between pairs or groups of proteins. Understanding protein–protein interactions is important for the investigation of intracellular signaling pathways, modelling of protein complex structures and for gaining insights into various biochemical processes.
Computational biologyComputational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has foundations in applied mathematics, chemistry, and genetics. It differs from biological computing, a subfield of computer engineering which uses bioengineering to build computers. Bioinformatics, the analysis of informatics processes in biological systems, began in the early 1970s.
BioremediationBioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi, and plants), living or dead, is employed for removing environmental pollutants from air, water, soil, flue gasses, industrial effluents etc., in natural or artificial settings. The natural ability of organisms to adsorb, accumulate, and degrade common and emerging pollutants has attracted the use of biological resources in treatment of contaminated environment.
BiodegradationBiodegradation is the breakdown of organic matter by microorganisms, such as bacteria and fungi. It is generally assumed to be a natural process, which differentiates it from composting. Composting is a human-driven process in which biodegradation occurs under a specific set of circumstances. The process of biodegradation is threefold: first an object undergoes biodeterioration, which is the mechanical weakening of its structure; then follows biofragmentation, which is the breakdown of materials by microorganisms; and finally assimilation, which is the incorporation of the old material into new cells.
Cyclic compoundA cyclic compound (or ring compound) is a term for a compound in the field of chemistry in which one or more series of atoms in the compound is connected to form a ring. Rings may vary in size from three to many atoms, and include examples where all the atoms are carbon (i.e., are carbocycles), none of the atoms are carbon (inorganic cyclic compounds), or where both carbon and non-carbon atoms are present (heterocyclic compounds with rings containing both carbon and non-carbon).
Environmental remediationEnvironmental remediation deals with the removal of pollution or contaminants from environmental media such as soil, groundwater, sediment, or surface water. Remedial action is generally subject to an array of regulatory requirements, and may also be based on assessments of human health and ecological risks where no legislative standards exist, or where standards are advisory. In the United States, the most comprehensive set of Preliminary Remediation Goals (PRGs) is from the Environmental Protection Agency (EPA) Regional Screening Levels (RSLs).
Natural environmentThe natural environment or natural world encompasses all living and non-living things occurring naturally, meaning in this case not artificial. The term is most often applied to Earth or some parts of Earth. This environment encompasses the interaction of all living species, climate, weather and natural resources that affect human survival and economic activity.
Polycyclic compoundIn the field of organic chemistry, a polycyclic compound is an organic compound featuring several closed rings of atoms, primarily carbon. These ring substructures include cycloalkanes, aromatics, and other ring types. They come in sizes of three atoms and upward, and in combinations of linkages that include tethering (such as in biaryls), fusing (edge-to-edge, such as in anthracene and steroids), links via a single atom (such as in spiro compounds), bridged compounds, and longifolene.
Rosetta (bioinformatics)Rosetta is a software package for protein structure prediction. Originally introduced by the Baker laboratory at the University of Washington in 1998 as an ab initio approach to structure prediction, Rosetta has since branched into several development streams and distinct services, providing features such as macromolecular docking and protein design. Many of the graduate students and other researchers involved in Rosetta's initial development have since moved to other universities and research institutions, and subsequently enhanced different parts of the Rosetta project.
ArsenicArsenic is a chemical element with the symbol As and atomic number 33. Arsenic occurs in many minerals, usually in combination with sulfur and metals, but also as a pure elemental crystal. Arsenic is a metalloid. It has various allotropes, but only the grey form, which has a metallic appearance, is important to industry. The primary use of arsenic is in alloys of lead (for example, in car batteries and ammunition). Arsenic is a common n-type dopant in semiconductor electronic devices.
Restoration ecologyRestoration ecology is the scientific study supporting the practice of ecological restoration, which is the practice of renewing and restoring degraded, damaged, or destroyed ecosystems and habitats in the environment by active human interruption and action. Ecological restoration can reverse biodiversity loss, combat climate change and support local and global economies.
MicroplasticsMicroplastics are fragments of any type of plastic less than in length, according to the U.S. National Oceanic and Atmospheric Administration (NOAA) and the European Chemicals Agency. They cause pollution by entering natural ecosystems from a variety of sources, including cosmetics, clothing, food packaging, and industrial processes. The term macroplastics is used to differentiate microplastics from larger plastic waste, such as plastic bottles or bigger pieces of plastics. Two classifications of microplastics are currently recognized.
