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CASTp
1. Introduction of CASTp Server Computer Atlas of Surface Topography of ProteinsCASTp aims to provide comprehensive and detailed quantitative characterization of topographic features of protein, is now updated to version 3.0. Since its release in 2006, the CASTp server has ~ 45 000 visits and fulfills ~ 33 000 calculation requests annually. CASTp has been proven as a confident tool for a wide range of researches, including investigations of signaling receptors, discoveries of cancer therapeutics, understanding of mechanism of drug actions, studies of immune disorder diseases, analysis of protein–nanoparticle interactions, inference of protein functions and development of high-throughput computational tools. This server is maintained bJie Liang's labin University of Illinois at Chicago. 2. Geometric Modeling Principles For the calculation strategy of CASTp, alpha-shape and discrete-flow methods are applied to the protein binding site, also the measurement of pocket size by the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of Illinois At Chicago
The University of Illinois Chicago (UIC) is a Public university, public research university in Chicago, Illinois. Its campus is in the Near West Side, Chicago, Near West Side community area, adjacent to the Chicago Loop. The second campus established under the University of Illinois system, UIC is also the largest university in the Chicago metropolitan area, having more than 33,000 students enrolled in 16 colleges. It is Carnegie Classification of Institutions of Higher Education, classified among "R1: Doctoral Universities – Very high research activity." The roots of UIC can be traced to the establishment of the Chicago College of Pharmacy in 1859, which was joined in the 1800s by additional medical related schools. It began an undergraduate program toward the end of World War II, and developed its West side campus in the 1960s. In 1982, it consolidated the University of Illinois at Chicago Circle and the University of Illinois at the Medical Center into the present universi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UCSF Chimera
UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and movies can be created. Chimera includes complete documentation and can be downloaded free of charge for noncommercial use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI) at the University of California, San Francisco. Development is partially supported by the National Institutes of Health (NIGMS grant P41-GM103311). The next-generation program is UCSF ChimeraX. General structure analysis * automatic identification of atom * hydrogen addition and partial charge assignment * high-quality hydrogen bond, contact, and clash detection * measurements: distances, angles, surface area, volume * calculation of centroids, axes, planes and associate ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Solvent Accessible Surface Area
The accessible surface area (ASA) or solvent-accessible surface area (SASA) is the surface area of a biomolecule that is accessible to a solvent. Measurement of ASA is usually described in units of square angstroms (a standard unit of measurement in molecular biology). ASA was first described by Lee & Richards in 1971 and is sometimes called the Lee-Richards molecular surface. ASA is typically calculated using the 'rolling ball' algorithm developed by Shrake & Rupley in 1973. This algorithm uses a sphere (of solvent) of a particular radius to 'probe' the surface of the molecule. Methods of calculating ASA Shrake–Rupley algorithm The Shrake–Rupley algorithm is a numerical method that draws a mesh of points equidistant from each atom of the molecule and uses the number of these points that are solvent accessible to determine the surface area. The points are drawn at a water molecule's estimated radius beyond the van der Waals radius, which is effectively similar to ‘rollin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Connolly Surface
The accessible surface area (ASA) or solvent-accessible surface area (SASA) is the surface area of a biomolecule that is accessible to a solvent. Measurement of ASA is usually described in units of square angstroms (a standard unit of measurement in molecular biology). ASA was first described by Lee & Richards in 1971 and is sometimes called the Lee-Richards molecular surface. ASA is typically calculated using the 'rolling ball' algorithm developed by Shrake & Rupley in 1973. This algorithm uses a sphere (of solvent) of a particular radius to 'probe' the surface of the molecule. Methods of calculating ASA Shrake–Rupley algorithm The Shrake–Rupley algorithm is a numerical method that draws a mesh of points equidistant from each atom of the molecule and uses the number of these points that are solvent accessible to determine the surface area. The points are drawn at a water molecule's estimated radius beyond the van der Waals radius, which is effectively similar to ‘rolling ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PyMOL
PyMOL is an open source but proprietary molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. As the original software license was a permissive licence, they were able to remove it; new versions are no longer released under the Python license, but under a custom license (granting broad use, redistribution, and modification rights, but assigning copyright to any version to Schrodinger, LLC.), and some of the source code is no longer released. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, by 2009, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL. PyMOL ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
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. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteomics
Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body. The proteome is the entire set of proteins produced or modified by an organism or system. Proteomics enables the identification of ever-increasing numbers of proteins. This varies with time and distinct requirements, or stresses, that a cell or organism undergoes. Proteomics is an interdisciplinary domain that has benefited greatly from the genetic information of various genome projects, including the Human Genome Project. It covers the exploration of proteomes from the overall level of protein composition, structure, and activity, and is an important component of functional genomics. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Structural Biology
Structural biology is a field that is many centuries old which, and as defined by the Journal of Structural Biology, deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every level of organization. Early structural biologists throughout the 19th and early 20th centuries were primarily only able to study structures to the limit of the naked eye's visual acuity and through magnifying glasses and light microscopes. In the 20th century, a variety of experimental techniques were developed to examine the 3D structures of biological molecules. The most prominent techniques are X-ray crystallography, nuclear magnetic resonance, and electron microscopy. Through the discovery of X-rays and its applications to protein crystals, structural biology was revolutionized, as now scientists could obtain the three-dimensional structures of biological molecules in atomic detail. Likewise, NMR spectroscopy allowed information about p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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