74 Open source projects that are alternatives of or similar to caviar

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

VSCode Extension for interactively visualising protein structure data in the editor

Protein structure comparison tools such as SSAP and SNAP

Utility to resolve SQL Server callstacks to their correct symbolic form using just PDBs and without a dump file

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

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

waka waka

Pytorch/Python3 implementation of DeepAccNet, protein model accuracy evaluator.

Remote vanilla PDB (over TCP sockets).

.NET Decompiler with support for PDB generation, ReadyToRun, Metadata (&more) - cross-platform!

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

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

MOLeculAR structure annoTator

RosettaDesign using PyRosetta

A suite of tools to explore protein structures with Protein Blocks 🐍

Neural Networks for Protein Sequence Alignment

A tool to make Windows builds reproducible.

PDB parser in Haskell

PDBRipper is a utility for extract an information from PDB-files.

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

A parser for Microsoft PDB (Program Database) debugging information

Syntax highlighting for computational biology

Fetch PDB symbols directly from Microsoft's symbol servers

A Python API for the RCSB Protein Data Bank (PDB)

Monte Carlo and Molecular Dynamics Simulation Package

Differentiable molecular simulation of proteins with a coarse-grained potential

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

View proteins and trajectories in the terminal

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..

📚 🔬 PIA - Protein Inference Algorithms

Some useful Tips and Tricks to speed up the data analysis process in Python.

ProtVec can be used in protein interaction predictions, structure prediction, and protein data visualization.

Single Page Web Application for displaying and studying molecular models

Graph Network for protein-protein interface

Guided Conditional Wasserstein GAN for De Novo Protein Design

Syntax highlighting for computational biology

TeamCity Symbol Server plugin

Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format

Protein Secondary Structure predictor using Convolutional Neural Networks

Pdb and Vim integration

Template with code & dataset for the "Structural basis for solubility in protein expression systems" challenge at the Copenhagen Bioinformatics Hackathon 2021.

Tool for PDB generation from IDA Pro database

Application to assign secondary structure to proteins

A cheatsheet for the Python Debugger (pdb)

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

Full-screen console debugger for Python

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

📖 mmCIF support for hybrid/integrative models

pdb + Rich library

Converts between Windows PDB and Portable PDB formats.

Pytest PuDB debugger integration

Modelling the Language of Life - Deep Learning Protein Sequences

NoPdb: Non-interactive Python Debugger

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

Fast and flexible ORF finder

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

Benchmarking common tasks on proteins in various languages and packages

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.