77 Open source projects that are alternatives of or similar to mmterm

🧬 An R package for visualizing molecular data in 3D

Neural Networks for Protein Sequence Alignment

Official git repository for Biopython (originally converted from CVS)

Modelling the Language of Life - Deep Learning Protein Sequences

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

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.

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.

Predicting protein structure through sequence modeling

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

The specification of the MMTF format for biological structures

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

Trajectory Tracking Project

An utf-8/truecolor image and video viewer for the terminal

Inverse Kinematics Engine for the Franka Emika Panda for Cartesian Pose Control.

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

waka waka

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

Modeling molecular ensembles with scalable data structures and parallel computing

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

Inference of couplings in proteins and RNAs from sequence variation

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

A simplified drug discovery pipeline -- generating SMILE molecular with AlphaSMILES, predicting protein structure with AlphaFold, and checking the druggability with fpocket/Amber.

Protein cavity identification and automatic subpocket decomposition

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

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

Graph Network for protein-protein interface

MOLeculAR structure annoTator

Protein structure comparison tools such as SSAP and SNAP

2D & 3D graphics engine in the terminal [C/C++]

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

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.

Protein Secondary Structure predictor using Convolutional Neural Networks

An efficient image pixelizer written in go

De novo protein structure prediction using iteratively predicted structural constraints

Recurrent Geometric Network in Pytorch

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

Formed trajectories of sets of points.Experimented on finding similarities between trajectories based on DTW (Dynamic Time Warping) and LCSS (Longest Common SubSequence) algorithms.Modeled trajectories as strings based on a Grid representation.Benchmarked KNN, Random Forest, Logistic Regression classification algorithms to classify efficiently t…

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

An open-source platform for developing protein models beyond AlphaFold.

An all-atom protein structure dataset for machine learning.

Evolutionary couplings from protein and RNA sequence alignments

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

Fast and flexible ORF finder

Paratope Prediction using Deep Learning

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

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

📚 🔬 PIA - Protein Inference Algorithms

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

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

PDB parser in Haskell

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

Python package designed for collecting and processing trajectory data.

Perception-Aware Trajectory Planner in Dynamic Environments

Fully convolutional neural networks for protein residue-residue contact prediction

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.

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

The World's First Search Engine for Trajectory Data

3D hotspot mutation proximity analysis tool