Search Results for "pdb file"
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Showing 84 open source projects for "pdb file"
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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. It interfaces with multiple chemistry formats and data sources, making it a... -
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iCn3D
Web-based protein structure viewer and analysis tool
...The complete package of iCn3D including Three.js and jQuery is in the directory "dist" after you get the source code with the "Code" button. View a 3D structure in iCn3D, input a PDB ID, and click "Load". You can also click the "File" menu to "Open File" or input other IDs. You can open a browser in your Virtual Reality (VR) headset and view a 3D structure in iCn3D. Then click the button "Enter VR" at the bottom center of your browser to enter the VR view. You can select residues with the trigger button. -
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DBConvert is a cross converter for HanDBase-, List-, JFile-, MobileDB-, PilotDB-, MariaDB-, MySQL-, PostgreSQL-, SQLite-, MS-Access-, SQL Server-, Firebird- , DBase- and Foxpro- databases, as well as MS-Excel and Calc spreadsheets, CSV- , JSON-, vCard-, hCard-, jCard-, xCard-, YAML- and XML files. Source files: https://github.com/TvBreukelen/fnpdbservices
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MUI Extended
A bunch of unofficial icons based on Google's Material Design Icons.
A bunch of unofficial icons based on Google's Material Design Icons. This is not affiliated with, or made by Google. -
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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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Jmol
An interactive viewer for three-dimensional chemical structures.
...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. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. ... -
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Hydrogen Bond Analysis Tool (HBAT)
HBAT 2 is migrated from PERL to Python.
HBAT(Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. HBAT 2 is migrated from PERL to Python. Latest Documentation: https://hbat.abhishek-tiwari.com/ Web Server Version: http://hbat-web.abhishek-tiwari.com Latest Github Release: http://github.com/abhishektiwari/hbat Citation: Tiwari, A., & Panigrahi, S. K. (2007). HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal Structures. ... -
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GromacsProSuite
Graphical User Interface for Gromacs
This tool is an integrated graphical interface that simplifies molecular dynamics simulations using Gromacs. It provides a structured, tab-based environment to set up, execute, and analyze simulations data without complex command-line operations. The software automates tasks such as topology generation, solvation, ion addition, minimization, equilibration, and production runs while executing GROMACS commands in the background. Built-in monitoring tracks CPU, RAM, and disk usage to ensure... -
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Cecil
Cecil is a library to inspect, modify and create .NET programs
Cecil is a library to inspect, modify and create .NET programs and libraries. Mono.Cecil is a library to generate and inspect programs and libraries in the ECMA CIL form. Analyze .NET binaries using a simple and powerful object model, without having to load assemblies to use Reflection. Modify .NET binaries, add new metadata structures and alter the IL code. Cecil has been around since 2004 and is widely used in the .NET community. If you're using Cecil, or depend on a framework, project, or... -
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RedtDec
RetDec is a retargetable machine-code decompiler based on LLVM
The decompiler is not limited to any particular target architecture, operating system, or executable file format. ELF, PE, Mach-O, COFF, AR (archive), Intel HEX, and raw machine code supported. 32-bit: Intel x86, ARM, MIPS, PIC32, and PowerPC 64-bit: x86-64 supported. Demangling of symbols from C++ binaries (GCC, MSVC, Borland). Reconstruction of functions, types, and high-level constructs. Output in two high-level languages: C and a Python-like language. Generation of call graphs,... -
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AWS GameKit Plugin for Unreal
The AWS GameKit Plugin for Unreal
...Game projects created in Unreal versions later than 4.27 are not backward compatible. AWS GameKit supports Unreal Engine version 4.27. Create the Visual Studio Solution for your game. Build GameKit C++ and copy over the DLL/PDB files. Make sure to checkout the matching version from the .gkcpp_version file in this repository. -
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Vexed for Windows
Classic PalmPilot Vexed Puzzle newly coded for Windows
Vexed is a well known puzzle game challenging your ability to plan and think ahead to complete the puzzles made famous on the PalmPilot. Start off easy and work your way to the harder puzzle packs like the 'impossible', 'confusion', or 'panic' packs. Run Classic Vexed in Windows! Same level packs, new 'cleanroom' code for Windows implements all play features, plus more, of the original. Click sample images below to see the full window Install files are under the Files tab,... -
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LMAPper - The SPM and Mol Viewer
Where SPM images and molecular models meet
This application lets STM or AFM images AND molecular models to be overlaid. It is useful to understand how your molecules fit to what you observed and can help interpret your data. What makes this application more useful than paint programs (powerpoint or inkscape) is the fact that the size of the images and of the molecule is fixed, so that you know that you are working in real space. Check https://sourceforge.net/p/spm-and-mol-viewer/wiki/Home/ for updates. -
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silico
Libraries and scripts for molecular modelling written in Perl
A perl molecular toolkit designed to assist in general molecular modelling activities. Silico provides file format conversion, molecular manipulation and analysis and a simple way to write wrapper scripts around other preexisting software packages. -
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POWAINDv1.0
Protein Water Interactions Determination, version 1.0
Crystallographic shell-waters that originate from diffraction data are an essential component, but not bulk water, of protein structure and stability. It interacts with various polar and non-polar components of protein. Polar backbone is constituted by O-type and N-type atoms of all residues. Polar side-chains are O, N, S containing groups of amino acid residues. Notably, ordered shell-waters form bridge interactions. Disordered shell-water may occupy central hydrophobic-cavity of protein.... -
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Timer for speech and debate competitions. Keeps track of speech order, time limits, and prep time for various debate formats (Policy, LD, Parliamentary, Public Forum, etc.) and individual events. Gives verbal and visual time signals.
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Cool Reader
A cross-platform XML/CSS based eBook reader
CoolReader is fast and small cross-platform XML/CSS based eBook reader for desktops and handheld devices. Supported formats: FB2, TXT, RTF, DOC, TCR, HTML, EPUB, CHM, PDB, MOBI. Platforms: Win32, Linux, Android. Ported on some eInk based devices. -
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JSiteDescriptor
Binding site descriptor generation for SVM based classification.
A set of java programs that extract coordinate and chemical information from PDB files. The binding site regions are extracted using grid based scheme. For binding site, spatio-chemical descriptor is generated based on PocketMatch algorithm of Dr. Kalidas (author of this project too). -
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chops
Convex Hull Of Protein Surface
This program will calculate all k-th convex hulls of protein surface when input a protein pdb file (pdb format), it is supplied in source code form along with the required data files and run under the windows/linux. -
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vcproj2cmake
Visual Studio .vc[x]proj to CMakeLists.txt (make, Ninja ...) enabler
Elaborate Visual Studio .vcxproj / .vcproj projects to CMakeLists.txt converter, enabling Makefile or Ninja or IDE builds, i.e. full multi-platform CMake functionality (Linux, Mac, Windows...). Live Update capability: supports side-by-side tracking of evolving original proj files, within build tree!! Script hooks for static CMake defs, powerful definition-to-variable mapping. Access to project data content is via git repository _only_ (it's a developer infrastructure project, thus... -
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LinXTL is a text editor and a crystallographic toolbox for structural solution and refinement. It includes support for commonly used X-ray programs, makes it easer to generate publication materials and appendices for PhD thesis.
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chemfiles
Modern library for chemistry file reading and writing
Chemfiles is a modern and high-quality library for reading and writing trajectory files created by computational chemistry simulations program. These trajectories contains atomic positions, velocities, names, topology and sometimes more. Running simulations produce enormous amounts of data, which has to be post-processed to extract physical information about the simulated system. Chemfiles provides an interface to access this information which is - unified: the same code will work with... -
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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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PDBManip
PDBManip is a free program for editing PDB (Protein Data Bank) Files
PDBManip is a free program for editing and manipulating PDB (Protein Data Bank) files. It has a graphical user interface and it is provided as an executable file for running on Windows® operating systems. There is a bunch of free programs on the internet for the same purpose. What discriminate between PDBManip and those programs is that PDBManip uses AngelScript language which is very similar to C/C++ language, to write scripts to do our editing tasks. -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/
