/tools

Deep H3 Loop Prediction is a tool that utilizes a deep residual network architecture to predict probability distributions of inter-residue distances and angles specifically for CDR H3 loops in antibodies. It is designed to assist in the modeling and prediction of antibody structures based on sequence input.

AlphaFold 3 is a hackable inference pipeline for predicting the 3D structures of proteins from their amino acid sequences. It allows users to run predictions without the need for large databases or Docker, making it accessible for experimentation and research.

structRFM is an open-source structure-guided RNA foundation model designed for robust structural and functional inference. It integrates sequence and structural knowledge to achieve state-of-the-art performance in RNA secondary and tertiary structure prediction, as well as function prediction tasks.

The AlphaFold MCP Server is a comprehensive tool that allows users to access and analyze protein structure predictions from the AlphaFold Protein Structure Database. It offers features such as structure retrieval, confidence score analysis, and batch processing for multiple proteins, making it valuable for researchers in molecular biology and bioinformatics.

This repository provides a pipeline for evaluating protein structure diffusion models, assessing designability, diversity, and novelty of generated protein structures. It supports various evaluation metrics and models, making it a useful tool for protein design and analysis.

ProtProfileMD is a tool that leverages protein dynamics to enhance homology detection by predicting per-residue distributions over structural representations. It utilizes a sequence-to-3D-probability model to capture the flexibility of proteins, improving the sensitivity of remote homology detection.

PolyFold is an interactive visual simulator designed for distance-based protein folding. It allows users to visualize and manipulate the folding process in real-time, utilizing stochastic optimization algorithms to achieve protein structure predictions.

DiffPALM is a tool for pairing interacting protein sequences using masked language modeling. It employs a differentiable pairing method to optimize multiple sequence alignments, which is crucial for understanding protein interactions and structures.

NetSurfP 3.0 is a tool designed for predicting protein secondary structures and solvent accessibility using advanced machine learning techniques. It utilizes embeddings from a pretrained model to enhance prediction accuracy and is implemented in PyTorch.

AlphaFind is a web-based search engine that enables users to discover structural similarities among proteins in the AlphaFold Protein Structure Database. It accepts various protein identifiers as input and provides similarity metrics and 3D visualizations of protein structures.

ADFLIP is a tool for all-atom inverse protein folding using discrete flow matching techniques. It allows users to sample protein sequences from input files, facilitating the design and prediction of protein structures.

This repository provides a method to run AlphaFold in batch mode using multiprocessing, allowing for efficient prediction of protein structures. It is designed to handle multiple structures simultaneously, enhancing the usability of AlphaFold for large-scale protein design tasks.

PyMissense is a tool that generates pathogenicity plots and modified PDB files for custom proteins based on the AlphaMissense paper. It helps identify critical regions in amino acid chains that affect protein function and visualizes pathogenicity predictions.

AWS RoseTTAFold is a tool that facilitates the prediction of protein structures using the RoseTTAFold algorithm on AWS Batch. It includes Jupyter notebooks for submitting protein sequences for analysis, leveraging high-performance computing resources to optimize the prediction process.

EMBER2 is a tool for predicting protein structures without the need for sequence alignment, utilizing protein language models. It allows users to generate PDB structures from predicted distograms and provides predictions for human proteins.

OPUS-Fold is an open-source framework designed for protein folding based on torsion-angle sampling. It integrates various methods for protein structure prediction and allows for efficient modeling of protein side chains during the folding process.

The mlx-esm repository provides an implementation of Meta's ESM-1 protein language model using the MLX library. It allows users to generate new protein sequences and predict masked amino acids, contributing to protein design and structure prediction in molecular biology.

PySSA is a Python client designed for visual protein sequence to structure analysis, enabling users to predict and analyze 3D protein structures. It integrates with PyMOL and ColabFold, making protein structure prediction accessible for research and educational purposes.

Bridge-IF is an implementation of a model for learning inverse protein folding using Markov Bridges. It utilizes datasets related to protein structures to train and evaluate the model for generating protein sequences based on their structures.

The pmpnndiff repository provides an implementation of discrete diffusion for inverse protein folding, including pre-trained models and training routines. It aims to facilitate protein folding predictions and experiments, making it a valuable tool in molecular design.

Prospr is a toolbox designed for protein structure prediction using the HP-model. It includes various prediction algorithms, a protein data structure for simulating folding, and datasets for research in protein folding and structure analysis.

FMol is a simplified drug discovery pipeline that generates SMILE molecular representations using AlphaSMILES, predicts protein structures with AlphaFold, and evaluates druggability using fpocket and Amber. It integrates various molecular modeling techniques to facilitate drug discovery processes.

XtalNet is an end-to-end tool for predicting crystal structures based on Powder X-Ray Diffraction data. It utilizes advanced deep learning techniques to generate and evaluate crystal structures, making it significant for materials science and molecular modeling.

The _map_align_ tool aligns two contact maps to maximize overlapping contacts while minimizing gaps. It allows users to input contact maps and template libraries, facilitating the alignment of protein structures based on contact information.