/tools

py2Dmol is a Python library designed for visualizing protein, DNA, and RNA structures in 2D, suitable for use in Google Colab and Jupyter notebooks. It allows users to load and display molecular structures interactively, making it a useful tool for molecular representation.

oxDNA is a simulation code designed for modeling DNA and RNA using a coarse-grained approach. It provides an extensible framework for simulating various molecular interactions and dynamics, supporting both single CPU and GPU computations.

LucaVirus is a tool designed to model the evolutionary and functional landscape of viruses using a unified genome-protein language model. It provides datasets of viral sequences and supports various tasks such as predicting protein properties and classifying viral sequences.

The MycoplasmaGenitalium repository provides tools and models for simulating and visualizing the structure of Mycoplasma genitalium, including DNA and protein configurations. It utilizes cellPACKgpu for generating 3D models and integrates data from computational models to facilitate molecular modeling.

BinderFlow is a pipeline for designing protein binders, allowing users to manage and monitor the design process efficiently. It includes features for batch processing, design filtering, and integration with DNA synthesis workflows.

CaLM is a codon adaptation language model designed to provide embeddings for DNA sequences, specifically aimed at enhancing protein engineering efforts. It allows users to embed sequences, which can be useful for predicting and optimizing protein properties.

LLM4Mol is a repository that explores the application of large language models in molecular design and protein research. It serves as a hub for studies and techniques that leverage AI to advance understanding in molecular properties and material science.

Mjolnir is a flexible and efficient coarse-grained molecular dynamics simulation package that supports various simulation algorithms and interactions. It is designed to facilitate the implementation of new forcefields and is suitable for simulating proteins and DNA.

do_x3dna is a tool designed for analyzing the dynamics of DNA and RNA structures during molecular dynamics simulations. It provides functionalities to calculate structural descriptors and analyze fluctuations in molecular trajectories.

LightDock is a docking framework that utilizes the Glowworm Swarm Optimization algorithm to facilitate protein-protein, protein-peptide, and protein-DNA docking. It allows users to define custom scoring functions and supports various simulation options, making it a versatile tool for molecular docking studies.

BagPype is a Python package designed for constructing atomistic, energy-weighted graphs from biomolecular structures. It allows for detailed modeling of molecular properties by incorporating various types of interactions, making it useful for studying proteins and nucleic acids.

EquiPNAS is a tool designed for predicting binding sites between proteins and nucleic acids (DNA/RNA) using equivariant deep graph neural networks. It provides methods for training and testing models specifically tailored for protein-DNA and protein-RNA interactions.

MetalDock is an open-source software tool that facilitates the docking of metal-organic complexes with proteins, DNA, and other biomolecules. It is designed to support research in molecular interactions involving transition metals.

Open3SPN2 is an implementation of the 3SPN2 and 3SPN2.C coarse-grained molecular models of DNA designed for use with OpenMM. It facilitates molecular simulations and dynamics, particularly focusing on DNA and its interactions with proteins.

RFDpoly is a diffusion-based machine learning model that facilitates the de novo design of various polymers, including DNA, RNA, and proteins. It provides tools for generating molecular structures and optimizing their designs, making it a valuable resource in molecular biology and computational chemistry.

Genos is a collection of foundation models designed for genomic sequence analysis, capable of handling long sequences and providing insights into gene elements and regulatory interactions. It supports various genomic tasks, including mutation prediction and cross-species classification, making it a valuable tool for researchers in molecular biology.

dash_ngl is a customized Dash component designed for visualizing molecular structures, particularly proteins and DNA. It allows users to select proteins via a dropdown and supports .pdb and .cif file formats, making it a useful tool for molecular representation.

DEL_analysis provides code to analyze data from DNA-encoded libraries, including data preparation, similarity calculations, and activity predictions for new compounds. It is designed to facilitate the analysis of experimental data from DEL screens.

DECL-Gen is a toolkit designed for creating and evaluating DNA encoded libraries. It facilitates the generation of combinatorial libraries in situ and aids in analyzing next generation sequencing results from library enrichments.

The DELTA-Toolkit is a software package for analyzing DNA-encoded library data, focusing on quality control, sequence analysis, and feature identification. It supports drug discovery efforts by providing insights into DNA binding motifs and other molecular characteristics.

The 'decode' tool is designed to decode and analyze next-generation sequencing (NGS) data from DNA-Encoded Library screenings. It allows users to specify encoding schemes and building block sequences, facilitating the analysis of molecular data related to DNA sequences.

NGS-Barcode-Count is a fast and memory-efficient tool designed to count and decode DNA barcodes from next-generation sequencing data. It is particularly useful for analyzing DNA encoded libraries and CRISPR sequencing, providing features like error handling and quality filtering.

Genome is a library designed for working with DNA, RNA, and other nucleic acids. It provides functionalities that are useful for molecular biology applications, particularly in the analysis and manipulation of genetic materials.

BioVIS is an interactive 3D molecular structure viewer that enables users to visualize and explore biomolecular structures such as proteins and DNA. Built with React and Three.js, it supports loading PDB files and offers features for detailed exploration and annotation of molecular structures.