128 Open source projects that are alternatives of or similar to hPDB

The specification of the MMTF format for biological structures

Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure

Protein Secondary Structure predictor using Convolutional Neural Networks

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

VSCode Extension for interactively visualising protein structure data in the editor

MOLeculAR structure annoTator

A library to open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files in Rust.

Haskell driver for Neo4j 3+ (BOLT protocol)

Compare the public API of different versions of a Hackage library

Converts between Windows PDB and Portable PDB formats.

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

OBJ file loader for golang

Benchmarking common tasks on proteins in various languages and packages

Just another tool to download specify Symbol (.pdb) files

Debug Python code within a Docker container remotely from your terminal using pudb

De novo protein structure prediction using iteratively predicted structural constraints

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

The repository pymolschortucts contains the a collection of shortcuts that are loaded on startup of PyMOL. These shortcuts enable websearches from within PyMOL as well as many other convienent functions that make work in PyMOL more productive..

Albis: High-Performance File Format for Big Data Systems

Rosetta FunFolDes – a general framework for the computational design of functional proteins.

A MIME type sniffer for Go.

Maybe one day a WINE-style implementation of the classic Mac Toolbox.

Neuroscience information exchange format

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)

A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto

View proteins and trajectories in the terminal

MagicaVoxel File Writer dependency free cpp class

Haskell bindings to SDL2_image.

A Microsoft Windows application that displays the contents of the file header of *.Gbx files used by the Nadeo game engine GameBox.

TeamCity Symbol Server plugin

Remotely and collaboratively debug your Python application via an IRC channel.

Application to assign secondary structure to proteins

Analyze zipfile, either local, or from url

Predicting protein structure through sequence modeling

Fetch PDB symbols directly from Microsoft's symbol servers

Fully convolutional neural networks for protein residue-residue contact prediction

Email address validation for Haskell

C++ library for MP4 file parsing.

NoPdb: Non-interactive Python Debugger

C/C++ library to handle writing simple Matlab(r) MAT file

A pure Java HDF5 library

Guided Conditional Wasserstein GAN for De Novo Protein Design

A collection of useful tutorials for Protein Science

Implementation of Geometric Vector Perceptron, a simple circuit for 3d rotation equivariance for learning over large biomolecules, in Pytorch. Idea proposed and accepted at ICLR 2021

Neural Networks for Protein Sequence Alignment

lightweight TIFF reader/writer library (C/C++)

Modeling molecular ensembles with scalable data structures and parallel computing

Reference documentation for the iOS Shortcuts app file structure

An all-atom protein structure dataset for machine learning.

3D hotspot mutation proximity analysis tool

Interchange format for results for static analysis tools

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

Protein structure comparison tools such as SSAP and SNAP

💾 OLE File Container Format

A dependency-free cross-platform swiss army knife for PDB files.

Single Page Web Application for displaying and studying molecular models

A fast and easy-to-use PLY parsing library in a single c++11 header and cpp file

FoLiA: Format for Linguistic Annotation - FoLiA is a rich XML-based annotation format for the representation of language resources (including corpora) with linguistic annotations. A wide variety of linguistic annotations are supported, making FoLiA a useful format for NLP tasks and data interchange. Note that the actual Python library for proces…

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

RosettaDesign using PyRosetta