Search Results for "pdb"
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Showing 151 open source projects for "pdb"
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Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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Stop Cyber Threats with VM-Series Next-Gen Firewall on AzureGain integrated visibility across all traffic in a single pass. Deploy Palo Alto Networks VM-Series to determine application identity and content while automating security policy updates via rich APIs.
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ChatDBG
ChatDBG - AI-assisted debugging. Uses AI to answer 'why'
ChatDBG is an AI-assisted debugging tool that integrates large language models into standard debuggers like pdb, lldb, and gdb. It allows developers to engage in a dialog with the debugger, asking open-ended questions about their program's behavior, and provides error diagnoses and suggested fixes. -
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ILSpy
.NET Decompiler with support for PDB generation, ReadyToRun, Metadata
ILSpy is the open-source .NET assembly browser and decompiler. Visual Studio 2022 ships with decompilation support for F12 enabled by default (using our engine v7.1). In Visual Studio 2019, you have to manually enable F12 support. Go to Tools / Options / Text Editor / C# / Advanced and check Enable navigation to decompiled source. C# for Visual Studio Code ships with decompilation support as well. To enable, activate the setting "Enable Decompilation Support. ILSpy is distributed under the... -
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Protenix
A trainable PyTorch reproduction of AlphaFold 3
Protenix is an open-source, trainable PyTorch reimplementation of AlphaFold 3, developed by ByteDance with the goal of democratizing high-accuracy protein structure prediction for computational biology and drug-discovery research. Protenix provides a complete pipeline for turning protein sequences (with optional MSA / sequence alignment) or structural inputs (e.g. PDB/CIF) into full 3D atomic-level structure predictions. It supports both “full” models and lightweight variants such as “Protenix-Mini,” offering a trade-off between speed/compute cost and predictive accuracy — making structure prediction accessible even in resource-constrained environments. The project also includes support for constraints (e.g., specifying residue- or atom-level contact constraints, or pocket constraints) to guide predictions toward biologically or experimentally relevant conformations, which enhances its utility for tasks like modeling complexes, ligands, or antibody–antigen interactions. -
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x64dbg
An open-source x64/x32 debugger for windows
...User database (JSON) for comments, labels, bookmarks, etc. Plugin support with growing API. Extendable, debuggable scripting language for automation. Multi-datatype memory dump. Basic debug symbol (PDB) support. Dynamic stack view. Built-in assembler (XEDParse/asmjit). Executable patching and analysis. We provide both the executable and the source. Feel free to contribute. Write plugins in C++, change colors and tweak your preferences. x64dbg can debug both x64 and x32 applications. There is only one interface. -
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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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GraphQL for .NET
This is an implementation of Facebook's GraphQL in .NET
...A GraphQL service is created by defining types and fields on those types, then providing functions for each field on each type. All packages generated from this repository come with embedded pdb and support Source Link. If you are having difficulty understanding how the code works or have encountered an error, then it is just enough to enable Source Link in your IDE settings. Then you can debug GraphQL.NET source code as if it were part of your project. The Schema first approach relies upon the GraphQL schema language, coding conventions, and tries to provide a minimal amount of syntax. ... -
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KOReader
An ebook reader application supporting PDF, DjVu, EPUB, FB2, etc.
KOReader is a document viewer for E Ink devices. Supported fileformats include EPUB, PDF, DjVu, XPS, CBT, CBZ, FB2, PDB, TXT, HTML, RTF, CHM, DOC, MOBI and ZIP files. It’s available for Kindle, Kobo, PocketBook, Android and desktop Linux. Runs on embedded devices (Cervantes, Kindle, Kobo, PocketBook, reMarkable), Android and Linux computers. Developers can run a KOReader emulator in Linux and MacOS. Multi-lingual user interface with a highly customizable reader view and many typesetting options. ... -
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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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x64dbg
An open-source x64/x32 debugger for windows.
An open-source x64/x32 debugger for windows. Development is done on GitHub (https://github.com/x64dbg/x64dbg). Daily snapshots are uploaded here, snapshots for every commit can be found on http://releases.x64dbg.com -
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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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A simple book reader for android. This reader is develop for Chinese book reading. It can display book in traditional style, right to left and top to bottom.It can open txt, html, epub, pdb(Haodoo), srb(book build for simplereader with notes inside)
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CemCon
Automated SMILES-to-optimized 3D molecular structure converter
CemCon is a desktop application developed for automated batch conversion of SMILES strings into optimized 3D molecular structures. The software is designed to simplify ligand preparation workflows for molecular docking, virtual screening, molecular dynamics simulations, and other Computer-Aided Drug Design (CADD) applications. Developed by Abhijit Reang and Sandip Das under the supervision of Dr. Arabinda Ghosh, Department of Molecular Biology and Bioinformatics, Tripura University,... -
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We developed IBEIP, an intelligent and accurate tool for identifying B cell dominant epitope regions based on Ag-nAb complex crystal structures from PDB database. During epitope mapping, IBEIP analyzes four molecular interactions (van der Waals forces, buried surface area, hydrogen bonds, and electrostatic interactions) between antigen and antibody complexes to ensure accuracy. IBEIP uses a hierarchical iterative merging model to merge highly overlapping epitopes and identify the hot nAb binding region as the B cell dominant epitope region. ...
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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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Genetic algorithm for EOM
A python GA code for EOM in SAXS/WAXS
Because GAjoe of ATSAS cannot deal with WAXS range, and no parameters can be modified. I made a code by myself to use GA for finding best EOM for SAXS/WAXS. The project need ATSAS crysol and a folder with multiple pdb files to use. -
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Cecil
Cecil is a library to inspect, modify and create .NET programs
...If you're using Cecil, or depend on a framework, project, or product using it, please consider sponsoring Cecil. Cecil 0.10 beta 5 addresses a long standing issue: previously, a rewrite of native pdb files would lose some debugging information, including the list of namespaces that were used in methods (and thus breaking the expression evaluation) or the scopes in generators (for iterators or async methods). -
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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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MOF-VR is a virtual reality program developed for Microsoft Windows and HTC Vive that allows for hypothetical metal-organic frameworks (MOFs) to be constructed and tested in molecular dynamics simulations of guest molecules.
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Vexed for Windows
Classic PalmPilot Vexed Puzzle newly coded for Windows
...Click sample images below to see the full window Install files are under the Files tab, and all additional Puzzle Packs are under Files-PuzzlePacks. All original Puzzle Packs are ready, be sure to download from here. Each Puzzle Pack typically has 60 puzzles and are in an ini format not the pdb format. There are more than 2900 puzzles available! There is a PortableApps version under the Files tab /PortablePgm as well. Full feature version 0.7.5.3 (startup bug fix) released 12/08/2020 Also at https://www.oldergeeks.com/downloads/file.php?id=3529 with 3500+ downloads -
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CheUP
Gromacs Topology Builder - OPLS AA Based. Support many charge model
...Moreover, user can use own parameter as well as original OPLS parameter. Finally, user also can add and edit the topology within the software. Main Features: 1. Generate GROMACS OPLS AA topology and structure (PDB, GRO, MOL2, etc) 2. Support quantum calculation for determining charge (MOPAC7.1 is included) 3. Calculate CM1A – LBCC and CM5 Charge Model 4. Read many files formats structure using Open Babel library and Quantum Output (MOPAC7.1, ORCA, GAUSSIAN, FIREFLY) 5. Nice Ways Adding Hydrogen
