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Adaptive Sampling
Adaptive sampling is a technique used in computational molecular biology to efficiently simulate protein folding when coupled with molecular dynamics simulations. Background Proteins spend a large portion – nearly 96% in some cases – of their folding time "waiting" in various thermodynamic free energy minima. Consequently, a straightforward simulation of this process would spend a great deal of computation to this state, with the transitions between the states – the aspects of protein folding of greater scientific interest – taking place only rarely. Adaptive sampling exploits this property to simulate the protein's phase space in between these states. Using adaptive sampling, molecular simulations that previously would have taken decades can be performed in a matter of weeks. Theory If a protein folds through the metastable states A -> B -> C, researchers can calculate the length of the transition time between A and C by simulating the A -> B transition and the B -> C tran ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Molecular Biology
Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physical structure of biological macromolecules is known as molecular biology. Molecular biology was first described as an approach focused on the underpinnings of biological phenomena - uncovering the structures of biological molecules as well as their interactions, and how these interactions explain observations of classical biology. In 1945 the term molecular biology was used by physicist William Astbury. In 1953 Francis Crick, James Watson, Rosalind Franklin, and colleagues, working at Medical Research Council unit, Cavendish laboratory, Cambridge (now the MRC Laboratory of Molecular Biology), made a double helix model of DNA which changed the entire research scenario. They proposed the DNA structure based on previous research done by ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Protein Folding
Protein folding is the physical process by which a protein chain is translated to 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 to a linear chain of amino acids. At this stage the polypeptide lacks any stable (long-lasting) three-dimensional structure (the left hand side of the first figure). As the polypeptide chain is being synthesized by a ribosome, the linear chain begins to fold into its three-dimensional structure. Folding of many proteins begins even during translation of the polypeptide chain. Amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein (the right hand side of the figure ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Thermodynamic Free Energy
The thermodynamic free energy is a concept useful in the thermodynamics of chemical or thermal processes in engineering and science. The change in the free energy is the maximum amount of work that a thermodynamic system can perform in a process at constant temperature, and its sign indicates whether the process is thermodynamically favorable or forbidden. Since free energy usually contains potential energy, it is not absolute but depends on the choice of a zero point. Therefore, only relative free energy values, or changes in free energy, are physically meaningful. The free energy is a thermodynamic state function, like the internal energy, enthalpy, and entropy. The free energy is the portion of any first-law energy that is available to perform thermodynamic work at constant temperature, ''i.e.'', work mediated by thermal energy. Free energy is subject to irreversible loss in the course of such work. Since first-law energy is always conserved, it is evident that free energy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Phase Space
In dynamical system theory, a phase space is a space in which all possible states of a system are represented, with each possible state corresponding to one unique point in the phase space. For mechanical systems, the phase space usually consists of all possible values of position and momentum variables. It is the outer product of direct space and reciprocal space. The concept of phase space was developed in the late 19th century by Ludwig Boltzmann, Henri Poincaré, and Josiah Willard Gibbs. Introduction In a phase space, every degree of freedom or parameter of the system is represented as an axis of a multidimensional space; a one-dimensional system is called a phase line, while a two-dimensional system is called a phase plane. For every possible state of the system or allowed combination of values of the system's parameters, a point is included in the multidimensional space. The system's evolving state over time traces a path (a phase-space trajectory for the sy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Metastable State
In chemistry and physics, metastability denotes an intermediate energetic state within a dynamical system other than the system's state of least energy. A ball resting in a hollow on a slope is a simple example of metastability. If the ball is only slightly pushed, it will settle back into its hollow, but a stronger push may start the ball rolling down the slope. Bowling pins show similar metastability by either merely wobbling for a moment or tipping over completely. A common example of metastability in science is isomerisation. Higher energy isomers are long lived because they are prevented from rearranging to their preferred ground state by (possibly large) barriers in the potential energy. During a metastable state of finite lifetime, all state-describing parameters reach and hold stationary values. In isolation: *the state of least energy is the only one the system will inhabit for an indefinite length of time, until more external energy is added to the system (unique " ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Folding@home
Folding@home (FAH or F@h) is a volunteer computing project aimed to help scientists develop new therapeutics for a variety of diseases by the means of simulating protein dynamics. This includes the process of protein folding and the movements of proteins, and is reliant on simulations run on volunteers' personal computers. Folding@home is currently based at the University of Pennsylvania and led by Greg Bowman, a former student of Vijay Pande. The project utilizes graphics processing units (GPUs), central processing units (CPUs), and ARM processors like those on the Raspberry Pi for volunteer computing and scientific research. The project uses statistical simulation methodology that is a paradigm shift from traditional computing methods. As part of the client–server model network architecture, the volunteered machines each receive pieces of a simulation (work units), complete them, and return them to the project's database servers, where the units are compiled into an ov ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Hidden Markov Model
A hidden Markov model (HMM) is a statistical Markov model in which the system being modeled is assumed to be a Markov process — call it X — with unobservable ("''hidden''") states. As part of the definition, HMM requires that there be an observable process Y whose outcomes are "influenced" by the outcomes of X in a known way. Since X cannot be observed directly, the goal is to learn about X by observing Y. HMM has an additional requirement that the outcome of Y at time t=t_0 must be "influenced" exclusively by the outcome of X at t=t_0 and that the outcomes of X and Y at t handwriting recognition, handwriting, gesture recognition, part-of-speech tagging, musical score following, partial discharges and bioinformatics. Definition Let X_n and Y_n be discrete-time stochastic processes and n\geq 1. The pair (X_n,Y_n) is a ''hidden Markov model'' if * X_n is a Markov process whose behavior is not directly observable ("hidden"); * \operatorname\bigl(Y_n \ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Computational Biology
Computational 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. History Bioinformatics, the analysis of informatics processes in biological systems, began in the early 1970s. At this time, research in artificial intelligence was using network models of the human brain in order to generate new algorithms. This use of biological data pushed biological researchers to use computers to evaluate and compare large data sets in their own field. By 1982, researchers shared information via punch cards. The amount of data grew exponentially by the end of the 1980s, requiring new computational methods for quickly interpreting ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Molecular Biology
Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physical structure of biological macromolecules is known as molecular biology. Molecular biology was first described as an approach focused on the underpinnings of biological phenomena - uncovering the structures of biological molecules as well as their interactions, and how these interactions explain observations of classical biology. In 1945 the term molecular biology was used by physicist William Astbury. In 1953 Francis Crick, James Watson, Rosalind Franklin, and colleagues, working at Medical Research Council unit, Cavendish laboratory, Cambridge (now the MRC Laboratory of Molecular Biology), made a double helix model of DNA which changed the entire research scenario. They proposed the DNA structure based on previous research done by ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Stanford University
Stanford University, officially Leland Stanford Junior University, is a Private university, private research university in Stanford, California. The campus occupies , among the largest in the United States, and enrolls over 17,000 students. Stanford is considered among the most prestigious universities in the world. Stanford was founded in 1885 by Leland Stanford, Leland and Jane Stanford in memory of their only child, Leland Stanford Jr., who had died of typhoid fever at age 15 the previous year. Leland Stanford was a List of United States senators from California, U.S. senator and former List of governors of California, governor of California who made his fortune as a Big Four (Central Pacific Railroad), railroad tycoon. The school admitted its first students on October 1, 1891, as a Mixed-sex education, coeducational and non-denominational institution. Stanford University struggled financially after the death of Leland Stanford in 1893 and again after much of the campus was ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Annual Review Of Biophysics
The ''Annual Review of Biophysics'' is a peer-reviewed scientific journal published annually by Annual Reviews. It covers all aspects of biophysics with solicited review articles. Ken A. Dill has been its editor since 2013. According to the ''Journal Citation Reports'', the journal has a 2021 impact factor of 19.763 ranking it first out of 72 journals in the category "Biophysics". History The ''Annual Review of Biophysics and Bioengineering'' was first published in 1972 by Annual Reviews in collaboration with the Biophysical Society. Its inaugural editor was Manuel F. Morales. In 1985, the name of the journal was changed to ''Annual Review of Biophysics and Biophysical Chemistry'', followed by another name change in 1992 to ''Annual Review of Biophysics and Biomolecular Structure''. In 2008 the journal obtained its current title. Abstracting and indexing The journal is abstracted and indexed in Scopus, Science Citation Index Expanded, BIOSIS Previews, Embase, MEDLINE, and Acad ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Molecular Modelling
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit (a molecular mechanics approach), or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons (a quantum chemistry approach). Molecular mechanics Molecular mechanics is one aspect of molecular modelling, as it involves the use of classical me ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |