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Dicey [15] is free software that outputs in-silico PCR products from primer sets provided in a FASTA file. It is fast (through use of a genome's FM-index) and can account for primer melting temperature and tolerated edit distances between primers and hit locations on the genome. VPCR [3] runs a dynamic simulation of multiplex PCR
Free open source: ms-2.de: OpenMM: No No Yes Yes Yes Yes No Yes Yes High Performance MD, highly flexible, Python scriptable Free open source MIT: OpenMM: Orac: No No Yes Yes No Yes No Yes No Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level Free open source: Orac download page ...
Agarose Gel simulation. Online Database searching - Search public databases at the NCBI such as Genbank and UniProt. Online BLAST searches. Protein analysis including estimation of Molecular Weight, Extinction Coefficient and pI. PCR Primer design, including an interface to Primer3; 3D structure viewing via an interface to Jmol
List of free analog and digital electronic circuit simulators, available for Windows, macOS, Linux, and comparing against UC Berkeley SPICE. The following table is split into two groups based on whether it has a graphical visual interface or not.
Scientific simulation software is used to simulate scientific phenomena based on a scientific model. Subcategories This category has the following 2 subcategories, out of 2 total.
A strip of eight PCR tubes, each containing a 100 μL reaction mixture Placing a strip of eight PCR tubes into a thermal cycler. The polymerase chain reaction (PCR) is a method widely used to make millions to billions of copies of a specific DNA sample rapidly, allowing scientists to amplify a very small sample of DNA (or a part of it) sufficiently to enable detailed study.
The term on-line simulation sometimes refers to server-side web-based simulation, sometimes to symbiotic simulation, i.e. a simulation that interacts in real-time with a physical system. The upcoming cloud-computing technologies can be used for new server-side simulation approaches.
Schrödinger's software tools include molecular dynamics simulations, free energy calculations, quantum mechanics calculations, and virtual screening tools. The company also offers consulting services and collaborates with partners in the industry to advance the field of computational chemistry and drug discovery.