557 Open source projects that are alternatives of or similar to r3dmol

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

VSCode Extension for interactively visualising protein structure data in the editor

View proteins and trajectories in the terminal

Modelling the Language of Life - Deep Learning Protein Sequences

Guided Conditional Wasserstein GAN for De Novo Protein Design

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

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screenlamp is a Python toolkit for hypothesis-driven virtual screening

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Neural Networks for Protein Sequence Alignment

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React wrapper for ngl

Tinker9: Next Generation of Tinker with GPU Support

Fitness landscape exploration sandbox for biological sequence design.

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fast functionalisation of molecules

General purpose tools for high-throughput catalysis

A Go package for engineering organisms.

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

Macromolecular viewer for crystallographers (WebGL)

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

PDB parser in Haskell

R htmlwidgets for ToastUI libraries: grid, calendar and chart

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htmlwidget for frappe charts js library

A denoising diffusion probabilistic model (DDPM) tailored for conditional generation of protein distograms

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

Fast and flexible ORF finder

Embed htmlwidgets in Responsive iframe.

web-based protein structure viewer and analysis tool interactively or in batch mode

Protein structure comparison tools such as SSAP and SNAP

Htmlwidget to write SQL queries

Evolutionary couplings from protein and RNA sequence alignments

Quantum Package : a programming environment for wave function methods

adcc: Seamlessly connect your program to ADC

Free, open, highly extensible WebGIS platform

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

This is the main repository for the HackBio'2020 Virtual Internship Experience ❤️

Protein cavity identification and automatic subpocket decomposition

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.

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

pyQms, generalized, fast and accurate mass spectrometry data quantification

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

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

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

The Microbiome Interpretable Temporal Rule Engine

In silico chemical library engine for high-accuracy chemical property prediction

Fully convolutional neural networks for protein residue-residue contact prediction

Robust and scalable inference of cell lineages from gene expression data.

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..

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htmlwidget that binds d3js collapsible trees to R and Shiny to make an interactive search tool

Code and Data to accompany "Dilated Convolutions for Modeling Long-Distance Genomic Dependencies", presented at the ICML 2017 Workshop on Computational Biology