/tools

CATHe is a deep learning tool that utilizes protein sequence embeddings to detect remote homologues for CATH superfamilies. It achieves high accuracy in predicting protein classifications, making it a valuable resource for researchers in molecular biology and bioinformatics.

RNAvigate is a toolset designed for exploring and comparing chemical probing data and structure models of RNA. It offers an easy-to-use interface, particularly effective in Jupyter Notebooks, for documenting and sharing analyses related to RNA structures.

DeepAllo is a deep learning framework designed for predicting allosteric sites in proteins using a protein language model with multitask learning. It provides an inference pipeline that identifies potential allosteric pockets based on input protein structures.

VespaG is a fast predictor of single amino acid variant effects using protein language models. It leverages a large dataset of variants to provide accurate fitness predictions, making it useful for protein design and analysis.

The PS4 Dataset is the largest open-source dataset for predicting protein single sequence secondary structure. It includes methods for validation and evaluation of secondary structure prediction models, making it a valuable resource for researchers in protein structure prediction.

AlphaFold Analyser is a command line tool designed for rapid visualization of predictions made by AlphaFold2 and AlphaFold3. It generates publication-quality plots for predicted aligned error (PAE) and pLDDT scores, as well as creating PyMol sessions for structural analysis.

ProteStAr is a tool designed to efficiently compress and archive collections of protein structure files, including formats like PDB and mmCIF. It offers high compression ratios and supports various file types, making it useful for managing large datasets in protein research.

AllMetal3D is a tool designed to predict metal and water binding sites in proteins using 3D convolutional neural networks (3DCNNs). It provides functionalities for both local and server-based usage, facilitating research in protein structure and interactions.

The Bohrium Science Agent SDK allows developers to create AI-driven scientific agents that can perform tasks related to molecular dynamics simulations and bioinformatics analysis. It supports the orchestration of scientific workflows and provides a visual interface for molecular structure display.

pLMSNOSite is an ensemble-based tool designed to predict protein S-nitrosylation sites by integrating supervised word embedding and embeddings from a protein language model. It allows users to input protein sequences and receive predictions regarding potential modifications.

The repository includes Jupyter Notebooks that utilize the b2btools for predicting various biophysical properties of proteins, such as dynamics and folding propensities. It allows users to analyze both single protein sequences and multiple sequence alignments to explore their biophysical behavior.

CPIExtract is a software package that collects and harmonizes interaction data between small molecules and proteins from multiple databases. It provides pipelines for extracting interactions based on either compound or protein input, facilitating the analysis of compound-protein interactions.

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.

proteinviz is an open-source tool that predicts the 3D structure of proteins based on their amino acid sequences. It utilizes a protein folding model to generate PDB files and visualize the protein structures in a user-friendly interface.

The kissim_app repository provides tools for comparing structural pockets of kinases using the kissim fingerprint. It facilitates the analysis of kinase structures, which is essential for understanding protein interactions and potential drug targets.