Search Results for "molecules" - Page 3
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Showing 87 open source projects for "molecules"
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Animp is an OpenGL program to display movies of particles in motion where the movies are produced by adding calls to animp library routines to simulation code written in either C++ or Fortran. Animp can also display molecules read from PDB files.
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Calculates Natural Product(NP)-likeness of a molecule, i.e. the similarity of the molecule to the structure space covered by known natural products. NP-likeness is a useful criterion to screen compound libraries and to design new lead compounds. Maven dependancy: <dependency> <groupId>uk.ac.ebi.cheminformatics</groupId> <artifactId>NP-Likeness</artifactId> <version>2.1</version> </dependency> Required repository: <repositories> ...
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Truncate Trajectory (VMD plugin)
reduces the size of MD trajectories
... be also provided in the original trajectory files (if not please contact me: tevang3@gmail.com). In the current version you can define how many water molecules to keep but not other hetero compounds. If you want to keep other hetero compounds (e.g. ions, ligands, etc.) then you will have to keep ALL of them. In future versions you will be able to specify how many non-water hetero compounds to keep (development is under way). -
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Molecules
molecules
Molecules is an application for viewing three-dimensional renderings of molecules and manipulating them using your fingers. You can rotate the molecules by moving your finger across the display, zoom in or out by using two-finger pinch gestures, or pan the molecule by moving two fingers across the screen at once. These structures can be viewed in both ball-and-stick and spacefilling visualization modes. New molecules can be downloaded from either the RCSB Protein Data Bank (http... -
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XML Schema for Atoms, Molecules and Solids
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RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files.
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createSimulationBoxForLammps
create complex simulation box for lammps
Creating a complex model for Lammps is a headache for someone like me! A python written script, createSimulationBox.py, is created to make the pre-processing easier. If you are familiar with Lammps well, it will be so handy; if you are newbie, don't worry, because it only has 6 commands. Moreover, the models(element, molecules like water) are coded in the program, and you are free to contribute your model into this simulationBox creator! -
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molmol
MOLMOL is a molecular analysis and display program
MOLMOL was part of a collaboration project between BRUKER/Spectrospin and Prof. Wüthrich at ETH Zürich. MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of molecules, with special emphasis on biological macromolecules. The program has features that make it particularly useful for the study of protein or DNA structures determined by NMR. See the Wiki Home page for more details about the current MOLMOL Enhancement Project 2013... -
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CH5M3D
HTML5 program for drawing and editting molecular structures
This program uses a combination of HTML5 and javascript to interactively draw and edit 3-dimensional structures of small molecules. While several useful web pages are included that require no modification, library calls are documented and examples provided to show how more advanced web pages can be created. A paper describing this program is available at the Journal of Cheminformatics (http://www.jcheminf.com/content/5/1/46). -
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QSAR Qualitative Validation
Qualitative validation of QSAR models
The purpose of this program is to verify the ability of the QSAR/Pharmacophore model to distinguish significantly between the two classes (i.e. active and inactive molecules). It is based on calculation of different qualitative validation parameters such as sensitivity, specificity, precision, accuracy, and F-measure. -
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partitioning
The role of spatial partitioning in biochemical signaling.
This site hosts code investigating the role of spatial partitioning in biochemical signaling. We consider a network motif that is ubiquitous in membrane signaling. We numerically implement the exact solution to a stochastic model of the motif. We also simulate diffusion and reactions of molecules explicitly on a two-dimensional lattice. -
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This software has been designed to estimate the conformational entropy of single molecules from extended molecular trajectories.
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TreeLiker
TreeLiker is a collection of fast algorithms for working with complex
TreeLiker is a collection of fast algorithms for working with complex structured data in relational form. The data can, for example, describe large organic molecules such as proteins or groups of individuals such as social networks or predator-prey networks etc. The algorithms included in TreeLiker are unique in that, in principle, they are able to search given sets of relational patterns exhaustively, thus guaranteeing that if some good pattern capturing an important feature of the problem... -
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MetCore
Metabolomics Bioinformatics Tools
...-mass spectrometry (LC-MS), and comprehensive two-dimensional gas chromatography-mass spectrometry (GCxGC/TOF-MS). Each type of analysis affords limited analyte coverage of molecules present in a patient sample and therefore provides only a partial molecular profile for an individual patient. These diverse analytical data must be integrated with advanced bioinformatics methods for accurate evaluation of health and detection of disease susceptibility. -
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TrajLab
MATLAB based programs for trajectory simulations of molecules
TrajLab (which stands for TRAJectory LABoratory) consists of two sets of MATLAB program packages. While subproject MolDynSim deals with generation of molecular trajectories (and other aspects of molecular simulation), subproject MetaStable is dedicated to the analysis of molecular trajectories by detecting metastable conformations (as well as other analysis techniques). Note that each of the two sub-projects has its own SVN repository, wiki, tracker, etc: Probably TrajLab is the first... -
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ChEMBLspace
ChEMBLSpace explores the target-ligand network based on ChEMBL data.
.... The molecules that meet the created activity profile are displayed within the application and the full collection can be saved as an SD file. See publication page: http://bioinformatics.oxfordjournals.org/content/29/4/523 -
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NLOPredict is a nonlinear optical prediction and data analysis tool. Nonlinear optical measurements can yield information about the structure of crystals, and orientation of molecules at surfaces and interfaces.
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GuiTope
Identifies significant regions in proteins from peptide selections.
Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features... -
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An editor for small organic molecules, written in C using gtk+. It can read and write SMILES and cml and can save to dia's file format. It is suitable for creating chemical molecule diagrams for lower level chemistry/ochem lab reports.
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Disco (DIStribution of COnformations) is a software package for the estimation of solution conformations of organic molecules. It is rewritten form of NAMFIS method and can be used with the input files generated by Janocchio.
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This is an implementation of the adaptive biasing force method (ABF) in NAMD. The code for ABF was developed by Eric Darve, Stanford University. ABF is a method created by E. Darve and A. Pohorille to calculate the free energy of bio-molecules.
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3DMolvis is a tool designed to make easy learning of basic structure and function of biological molecules.
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The Chemical Structures Project is a set of 3D structures of molecules in CML format. Each file contains also some physical properties, which can be access using a web browser or a CML file reader.
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Analyzes water molecules in the protein data bank file to look for polygonal water structures by looking for H-bond connections. GUI with automatic statistics, and PDB polygon drawer for viewing in Coot (Separate x-ray modelling software) included.
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Quantum Monte Carlo algorithms expressed in Python. This code calculates electronic properties of atoms and molecules from first principles.