/tools

OpenCafeMol is a multi-platform molecular dynamics simulator that facilitates coarse-grained molecular dynamics simulations on GPU. It utilizes OpenMM and is designed to handle various molecular simulations, making it a valuable tool in computational chemistry.

This repository contains computational models that identify potential drugs for repurposing against SARS-CoV-2 by utilizing QSAR models and virtual screening techniques. It specifically targets Mpro inhibitors and includes curated data and predictions for FDA approved and experimental drugs.

ConveyorLC is a parallel virtual screening pipeline designed for docking and MM/GBSA calculations. It facilitates the preparation of receptors and ligands, as well as the execution of docking simulations, making it a valuable tool for drug discovery and molecular modeling.

This repository contains a Python script that generates helical wheel visualizations based on input peptide sequences. It is useful for visualizing the arrangement of amino acids in alpha-helices, aiding in protein design and analysis.

Kylin-V is a software package designed for time-dependent density matrix renormalization group (TD-DMRG) and vibrational heat-bath configuration interaction (VHCI) methods. It provides improved code for simulating molecular systems without requiring unstable external libraries.

Chemprop benchmarking scripts and data for v2 provide tools for evaluating the performance of molecular property prediction models. The repository includes various datasets and benchmarks related to molecular properties, facilitating research in computational chemistry and machine learning.

ProteinWatermark is a tool designed to enhance privacy in protein design by injecting watermarks into protein sequences. It aims to protect intellectual property and ensure traceability in biosecurity applications.

sc-rs is an open-source Rust implementation of the Shape Complementarity (SC) algorithm, designed to evaluate the compatibility of protein interfaces. It provides a command-line interface and library API for quick analysis and integration into other tools.

RosettaSilentToolbox is a Python library designed for the analysis and management of large populations of protein or nucleotide decoys. It is particularly useful for protein designers and developers looking to benchmark their methods against existing protocols.

GPT_protein_design is a pipeline for de novo protein design that utilizes a GPT-based generator and a transfer learning-based discriminator. It aims to generate novel proteins, such as antimicrobial peptides, by leveraging advanced machine learning techniques.

ProfileBFN is an implementation for steering protein family design through Profile Bayesian Flow. It allows for the generation and evaluation of protein sequences, making it a valuable tool in the field of molecular design.

Mol3D is a 3D interactive program designed for molecular dynamics simulations using classical force fields. It allows users to create and manipulate molecular systems, integrate equations of motion, and visualize the dynamics of molecules in a graphical interface.

This repository contains implementations for protein structure prediction using various optimization techniques, including molecular dynamics simulations and genetic algorithms. It aims to explore different approaches to improve the accuracy and efficiency of predicting protein folding.

The molecule-representation repository offers React components for rendering interactive 2D representations of molecules. It allows users to visualize molecular structures with features like zooming and highlighting specific atoms and bonds.

Bokehmol is a library that offers custom extensions for plotting molecules interactively using the Bokeh framework. It allows users to render molecular depictions on-the-fly from SMILES representations, facilitating easier visualization in web applications.

This repository contains source codes for a balance-evolution artificial bee colony algorithm aimed at optimizing protein structures. It utilizes a three-dimensional off-lattice model to enhance protein structure prediction and optimization processes.

This repository contains designs and evaluations for protein binders created during the AdaptyvBio competition. It utilizes various tools and models, including AlphaFold, to generate and assess the stability and binding potential of protein designs.

ISAMBARD is a tool designed for the analysis, model building, and rational design of proteins. It aims to facilitate the design of coiled-coil and collagen structures, making it relevant for molecular design applications.

GNN_UNet is a tool for multi-scale protein structure modeling that utilizes geometric graph U-Nets to capture complex protein interactions. It provides a framework for training models that can predict protein structures, making it relevant for computational biology and molecular modeling.

BOOM is a tool designed for data-driven molecule discovery, focusing on out-of-distribution predictions of molecular properties. It includes benchmarks for evaluating various machine learning models on their ability to generalize to unseen molecular properties.

The 'mlgf' repository provides tools for machine learning many-body Green's function calculations, enabling the prediction of various chemical properties derived from electronic structure data. It utilizes advanced machine learning algorithms to fit self-energy functionals and offers features for analyzing molecular excitation spectra.

This repository provides an introduction to small molecule drug design using structure-based techniques and interactive Jupyter notebooks. It covers ligand-based analysis, generative design with REINVENT4, and docking to analyze interactions with the Zika virus protease.

ALLSites is a deep learning framework that predicts protein binding sites using a transformer-based architecture combined with convolutional encoders. It utilizes advanced optimization techniques and pre-computed protein embeddings to enhance the accuracy of binding site predictions.