Search Results for "molecular 3d structures protein"
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Showing 40 open source projects for "molecular 3d structures protein"
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Avogadro 2
Avogadro libraries provide 3D rendering, visualization, and analysis
AvogadroLibs is the core C++ library behind Avogadro 2, an open-source molecular editor and visualization platform used in chemistry, materials science, and education. It provides the essential tools for constructing, analyzing, and visualizing molecular structures in 2D and 3D. Designed for extensibility, AvogadroLibs supports plugins for quantum chemistry computations, molecular mechanics, and surface rendering. -
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BioEmu
Inference code for scalable emulation of protein equilibrium ensembles
Biomolecular Emulator (BioEmu for short) is a model that samples from the approximated equilibrium distribution of structures for a protein monomer, given its amino acid sequence. By default, unphysical structures (steric clashes or chain discontinuities) will be filtered out, so you will typically get fewer samples in the output than requested. The difference can be very large if your protein has large disordered regions, which are very likely to produce clashes. ... -
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iCn3D
Web-based protein structure viewer and analysis tool
"I see in 3D" (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode using NodeJS scripts based on the npm package icn3d. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom displays can be saved in a short URL or a PNG image. The complete package of iCn3D including Three.js and jQuery is in the directory "dist" after you get the source code with the "Code"... -
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
- Molecular Docking Virtual Screening Tool To Aid In Drug Discovery Research. - Published in Wiley, Journal of Computational Chemistry . Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27390 - Developed with Synchronized functioning of Python and Batch scripts -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us -... -
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Software and codes created in "Laboratorio de Química Computacional" of "Facultad de Ciencias y Tecnología" of "Universidad de Carabobo"
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Chem-Parser
Molecule Sketcher and Immediate Parser to Excel, .SMI and 3D SDF
Chem-Parser is an intuitive and efficient utility designed to streamline the data curation process for QSAR (Quantitative Structure–Activity Relationship) modeling and cheminformatics workflows. This versatile tool allows users to draw chemical structures, parse multiple SMILES strings, and automatically populate a structured table with associated compound names and custom-defined value tags such as biological activity or physicochemical properties. By enabling rapid structure-to-data... -
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Jmol
An interactive viewer for three-dimensional chemical structures.
Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. ... -
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Kekule
Kekule is a molecular visualization app for the 64-bit Windows
Kekule is a fork of Roger Sayle's old 16-bit Windows 3.1 RasMol 2.6 app, last updated and released in 1995. Kekule is meant to aid high school and college chemistry students in their organic and inorganic chemistry studies by allowing you to visualize molecules in 3 dimensions on your laptops. This will greatly increase a chemistry student's understanding of molecules and their structures. -
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...Fermi surface; 8. Density-of-states and band-structure; 9. Charge/spin density, Charge density difference; 10. Vacuum level and work function; 11. Wave-function analysis; 12. Molecular-dynamics analysis; 13. Effective mass of carrier; 14. Symmetry finding and operations; 15. 3D band structures; More details can be found in its official website https://vaspkit.com.
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towhee
Framework that is dedicated to making neural data processing
...You can use our Python API to build a prototype of your pipeline and use Towhee to automatically optimize it for production-ready environments. From images to text to 3D molecular structures, Towhee supports data transformation for nearly 20 different unstructured data modalities. We provide end-to-end pipeline optimizations, covering everything from data decoding/encoding, to model inference, making your pipeline execution 10x faster. Towhee provides out-of-the-box integration with your favorite libraries, tools, and frameworks, making development quick and easy. ... -
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MOLS 2.0 is a free and open-source software package for peptide modeling and protein-ligand docking. Authors: Dr. D. Sam Paul, Dr. S. Nehru Viji, Dr. P. Arun Prasad, Dr. K. Vengadesan, Dr. N. Gautham. If you use MOLS 2.0 for publication, please cite - D. Sam Paul, N. Gautham, MOLS 2.0: software package for peptide modeling and protein–ligand docking, Journal of Molecular Modeling 22 (2016) 1–9. Publications related to MOLS 2.0: 1.
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HostDesigner
General purpose de novo molecular design software
Although many potential applications exist in chemistry and material science, software to allow the general application of de novo structure-based design methods in supramolecular chemistry was non-existent. To address this limitation we created HostDesigner, a code that builds and evaluates millions of molecules in minutes. This command line executable builds 3D molecular structures by covalently connecting user-defined input fragments with pre-computed hydrocarbon fragments from a library. The results are ranked with respect to desired geometric constraints defined by the user. See the User's Manual for further details including a list of literature citations for example applications. ... -
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Cell Paint
cellPAINT allows users to create living illustrations of biology.
cellPAINT is a free-form painting app that allows users to create their own living illustrations of cellular landscapes. There are currently several prototypes available: --cellPAINT_coronavirus includes a newly-redesigned user interface, and molecular building blocks for coronavirus, blood plasma, and a simple human cell --cellPAINT_exo includes hand-painted sprites created by Julia Jimenez during an internship, and also allows input of custom sprites through Mesoscope --cellPAINT_VR is... -
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SAMFF
A Refined Empirical Force Field to Model Protein-SAM Interactions
Understanding protein interaction with material surfaces is important for the development of nanotechnological devices. The structures and dynamics of proteins can be studied via molecular dynamics (MD) if the protein-surface interactions can be accurately modeled. Based on AMBER14 and GAFF, we systematically tuned the Lennard-Jones parameters of selected amino acid sidechains and the functional group of SAM with repeated metadynamics and umbrella sampling simulations. ... -
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irayMol
Molecular visualization
Analyses and Interactive visualizations of the structures, functions and actions of biomolecules including molecular surface computation, and protein-ligand interface and protein-ligand docking where the ligand could a small compound, a nucleic acid, membrane and other proteins, written in C++/Qt/openGL/GLSL with more than 125,000 lines of codes. In addition to Qt, the only external library needed is GSL everything else is coded from the scratch. -
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LP Molecular Viewer
ActiveX/ATL molecular viewer component
This is a ActiveX/ATL component that shows molecular structures in 3D. It can read atomistic .pdb and .xyz file formats. This control is made very simple and flexible. It may be useful for chemists or other scientists to put molecular structures in presentations such as power point, with the ability to rotate or zoom using the mouse. It can also be used in developing graphical user interface for molecular calculations, and in any programming IDE that allows insertion of ActiveX controls. ... -
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mol3d
A metapost macro for drawing 3D molecular structures
Mol3d is a macro using metapost language (https://www.tug.org/metapost.html) for producing vector graphics of 3D molecular structures. It is based on the m3D macro developed by Anthony Phan (http://www-math.univ-poitiers.fr/~phan/m3Dplain.html). -
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Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs. PLEASE NOTE: The Biskit source code as well as any later releases are now hosted on https://github.com/graik/biskit The sourceforge repo is only kept here for reference.
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Protein Contact Matrix Generator
Command line application to generate contact matrix from proteins (3D)
A protein contact matrix is 2D representation of the distances between amino acid residues in a 3D protein structure. Protein Contact Map Generator (PCMGen) is a command line tool which takes protein 3D structures (PDB format files) as input and computes contact distances between two chains (from single or two different proteins). These matrix files can be further visualised as Contact Maps using other visualization tools/ programs (like R-heatmaps). ... -
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gMol
gMol molecular graphics
We've moved to https://github.com/tjod/gMol/wiki gMol is an interactive visualization system used to display and manipulate 3-dimensional models of scientific data, such as molecular structures and surfaces. It contains both OpenGL and web browser widgets that enable flexible user interfaces. -
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New advanced technologies including the next-generation DNA, and information technology have significantly improved our capacities of developing biological knowledge and changing our understanding of diseases, phenotype and genotype. In this post-genomic context, protein sequence analysis is a key issue to better understand the evolutionary, structural and functional aspects. NeoPipe is a tool of analyzing a protein family , which consists of 8 steps concerning the search for homologous sequences in multiple databases (protein, 3D structures,…) and functional and structural annotations of clustered multiple alignment of complete sequences (MACS). ...
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NanoCap
Carbon Fullerene and Capped Nanotube Generator
NanoCap is a generic application for the construction of low energy fullerene and capped nanotube structures. It provides an ideal tool to accompany the study of finite carbon molecules using computer simulation. The implementation involves a standalone application which includes a GUI and allows for dynamic visual inspection through 3D rendering. In addition, the NanoCap core libraries can be used in custom Python scripts that enabled the user to produce structures in bulk or to include the... -
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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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X3DBio2
A visual analysis tool for biomolecular structure comparison
A major problem in structural biology is the recognition of differences and similarities between related three dimensional (3D) protein structures. X3DBio2 is a visual analysis tool for 3D biomolecular structure comparison that allows for a clear comparison between similar structures from various species, for elucidation of structural effects of mutations, and for assessment of snapshots from molecular dynamics trajectories. X3DBio2 is the second milestone in a larger project currently in progress. ... -
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GenLab abbreviation of Genetics Laboratory .It is a user-friendly bioinformatics tool to support your bioinformatics lab work. GenLab creates a software user-friendly environment, which makes users to make a large number of protein, DNA, and RNA sequence analysis and excellent graphical viewing. It also provides powerful environment for simulations of Protein 3D molecular models. GenLab typically provides: •User-friendly graphical tools used for finding and working with relevant regions of DNA, RNA, and protein sequences. •Full integration of data input, data management, calculation results. ...
