/tools

The proto-Nucleic Acid Builder (pNAB) is a software tool designed for modeling the 3D structures of nucleic acids, including DNA and RNA. It allows for the construction of nucleic acids with alternative backbones or nucleobases and evaluates candidate structures based on geometric and energetic criteria.

SynCodonLM is a codon language model designed to optimize coding DNA sequences by disentangling codon usage from protein-level semantics. It allows for the generation of natural-looking coding sequences and provides embeddings for DNA sequences, making it a useful tool in synthetic biology and molecular design.

Deliqc is a tool designed to measure and quantify the quality of DNA encoded libraries. It allows users to extract point mutations from sequencing data and visualize mutation rates, making it useful for molecular biology applications.

DEL_data contains code and notebooks for analyzing data from DNA-encoded libraries, facilitating the reproduction of analyses and figures for related publications. It includes functions for data preparation and analysis, making it useful for researchers in molecular biology and drug discovery.

This repository provides C++ codes for running Monte Carlo simulations to model the buckling response of actin filaments under compression. It focuses on coarse-grained simulations for biopolymers, particularly DNA, and analyzes the resulting probability distributions of filament configurations.

MAP_DNN is a PyTorch implementation designed for cell-based selection of DNA-encoded libraries. It utilizes machine learning techniques to analyze data from these libraries, which is relevant for applications in molecular biology and drug discovery.

The 'cosm_scripts' repository contains force field parameters and scripts designed for modeling coarse-grained DNA origami structures. It supports molecular dynamics simulations and provides supplementary tools for researchers in the field of molecular modeling.

PDA-Pred is a tool designed to predict the binding affinity between proteins and DNA using structure-based features. It allows users to input protein-DNA complexes and provides predictions based on various structural and functional classifications.

The rstudiopymolpysnips library contains Python code snippets designed to enhance productivity when using PyMOL in RStudio. It facilitates the visualization and manipulation of molecular structures, particularly proteins and nucleic acids, by allowing users to run PyMOL commands directly from RStudio.

Enigma2 is a tool for DNA sequence prediction utilizing transformer-based models, including a BERT-based model for classification and an AlphaFold-like model for structural prediction. It also incorporates a custom pipeline for fetching datasets from the NCBI database.

This repository provides tools and datasets for evaluating ligand-based similarity metrics and molecular fingerprints specifically for RNA-targeted small molecule discovery. It includes scripts for molecular docking and statistical analyses of various methods used in the context of nucleic acid binders.

Biopython is a collection of Python tools for computational molecular biology, enabling users to work with biological data, including sequences and structures of proteins, DNA, and RNA. It supports various functionalities that are essential for bioinformatics applications.

D2MD is a DNA-Drug Molecular Docking Suite designed to automate and batch process molecular docking studies. It includes tools for using AutoDock and AutoDock Vina, along with scripts for molecular dynamics simulations, making it a comprehensive tool for studying drug-target interactions.

KaScape is a data analysis tool for processing Next-Generation Sequencing (NGS) data, focusing on the analysis of random dsDNA pools and their binding properties. It includes functionalities for calculating relative binding energy and visualizing data.

MAPLE is a tool designed for the detection of low-frequency methylation haplotypes using specifically designed probes. It includes modules for probe design, data processing, and machine learning classification to enhance the sensitivity and efficiency of genomic analyses.

DEL-Analysis is a companion software for analyzing outputs from DNA encoded libraries, specifically designed to work with data generated from NGS-Barcode-Count. It includes methods for data normalization, background subtraction, and visualization of molecular data through 2D and 3D graphs.

NPanalysis is a tool designed to analyze the properties of two-component nanoparticles in molecular dynamics simulations. It calculates various properties such as connection matrices, cluster analysis, and radii of gyration, specifically for DNA-PEI nanoparticles but applicable to other nanoparticle types.

The hth-dna-db repository provides a database of helix-turn-helix (HTH) protein-DNA complexes along with their position-weight matrices. It includes source code for generating new databases, facilitating research in protein-DNA interactions.

Molecular-Visualization-PyMOL is a project that utilizes PyMOL to visualize the structure of the Histone protein (PDB: 6KIX). It includes the creation of an educational movie that highlights key structural elements and interactions within the protein and its associated DNA.

ModularNucleoid is a software tool designed to generate models of the minimal genome bacterium JCVI-Syn3A. It produces models that test hypotheses about transcription and genome distribution, utilizing molecular simulations and optimization techniques.

Biosaic is a tokenizer library designed for DNA and protein sequences, enabling the conversion of sequences into k-mers and embeddings. It supports model training use-cases with state-of-the-art encoding architectures inspired by AlphaFold-2.

Multimodal-cfDNA-AI is a framework designed for analyzing cell-free DNA fragments using a Transformer model to enhance cancer detection. It processes NGS reads and integrates multi-omic features to provide insights at the molecular level, making it relevant for molecular biology applications.

py2Dmol is a Python library designed for visualizing protein, DNA, and RNA structures in 2D. It is user-friendly and can be used in Google Colab and Jupyter environments, making it accessible for researchers and students in molecular biology and cheminformatics.

MD_ligands_binding_DNA is a repository that provides molecular simulations for 78 DNA-ligand systems using the AMBER force field. It includes a dataset of DNA-ligand complexes along with their experimental binding affinity values, making it useful for studies in molecular property prediction and simulations.