Best AI tools for< Molecular Biologist >

Deep Genomics is a company that uses artificial intelligence (AI) to develop RNA therapies for genetic diseases. The company's AI platform is designed to identify novel targets and evaluate thousands of possibilities to identify the best therapeutic candidates. Deep Genomics is currently developing BigRNA+, which will expand the number of mechanisms and genetic variants the company can pursue.

Allchemy is a resource-aware AI platform for drug discovery. It combines state-of-the-art computational synthesis with AI algorithms to predict molecular properties. Within minutes, Allchemy creates thousands of synthesizable lead candidates meeting user-defined profiles of drug-likeness, affinity towards specific proteins, toxicity, and a range of other physical-chemical measures. Allchemy encompasses the entire resource-to-drug design process and has been used in academic, corporate and classified environments worldwide to: Design synthesizable leads targeting specific proteins Evolve scaffolds similar to desired drugs Design “circular” drug syntheses from renewable materials Interface with and instruct automated synthesis platforms and optimize pilot-scale processes Operate “iterative synthesis” schemes Predict side reactions and create forensic “synthetic signatures” of hazardous/toxic molecules Design synthetic degradation and recovery cycles for various types of feedstocks and functional target molecules

Atomwise is an artificial intelligence (AI)-driven drug discovery company that uses machine learning to discover and develop new small molecule medicines. The company's AI engine combines the power of convolutional neural networks with massive chemical libraries to identify new drug candidates. Atomwise has a wholly owned pipeline of drug discovery programs and also partners with other pharmaceutical companies to co-develop drugs. The company's investors include prominent venture capital firms and pharmaceutical companies.

Atomwise is an AI-powered drug discovery company that uses machine learning to identify new small molecule medicines. The company's platform combines the power of convolutional neural networks with massive chemical libraries to discover new drug candidates. Atomwise has a portfolio of wholly owned and co-developed pipeline assets, and is backed by prominent investors.

Iambic Therapeutics is a cutting-edge AI-driven drug discovery platform that tackles the most challenging design problems in drug discovery, addressing unmet patient need. Its physics-based AI algorithms drive a high-throughput experimental platform, converting new molecular designs to new biological insights each week. Iambic's platform optimizes target product profiles, exploring multiple profiles in parallel to ensure that molecules are designed to solve the right problems in disease biology. It also optimizes drug candidates, deeply exploring chemical space to reveal novel mechanisms of action and deliver diverse high-quality leads.

Tempus is an AI-enabled precision medicine company that brings the power of data and artificial intelligence to healthcare. With the power of AI, Tempus accelerates the discovery of novel targets, predicts the effectiveness of treatments, identifies potentially life-saving clinical trials, and diagnoses multiple diseases earlier. Tempus's innovative technology includes ONE, an AI-enabled clinical assistant; NEXT, a tool to identify and close gaps in care; LENS, a platform to find, access, and analyze multimodal real-world data; and ALGOS, algorithmic models connected to Tempus's assays to provide additional insight.

Tempus is an AI-enabled precision medicine company that brings the power of data and artificial intelligence to healthcare. With the power of AI, Tempus accelerates the discovery of novel targets, predicts the effectiveness of treatments, identifies potentially life-saving clinical trials, and diagnoses multiple diseases earlier. Tempus' innovative technology includes ONE, an AI-enabled clinical assistant; NEXT, which identifies and closes gaps in care; LENS, which finds, accesses, and analyzes multimodal real-world data; and ALGOS, algorithmic models connected to Tempus' assays to provide additional insight.

HUAWEI Cloud Pangu is an AI tool designed for accelerating drug discovery by optimizing drug molecules. It offers features such as Molecule Search, Molecule Optimizer, and Pocket Molecule Design. Users can submit molecules for optimization and view historical optimization results. The tool is based on the MindSpore framework and has been visited over 300,000 times since August 23, 2021.

Genesis Therapeutics is an AI-powered drug discovery platform that leverages advanced molecular AI technology to unlock novel protein targets, explore untapped chemical space, and accelerate the development of critical new medicines. The company comprises a team of drug hunters, deep learning researchers, and software engineers working together to drive AI in biochemistry and discover new therapies for patients with severe disorders. Their pioneering approach combines 3D spatial graph modeling and cutting-edge molecular simulation to generate innovative drug candidates.

Lavo Life Sciences is an AI-accelerated crystal structure prediction application that helps in drug development by providing accurate predictions. The platform offers solutions to de-risk pipelines, optimize solid-state formulations, and avoid late-stage surprises using AI technology. Lavo Life Sciences combines the expertise of chemists and engineers in AI and computational chemistry to deliver innovative solutions for drug development teams. The application aims to reduce turnaround time for crystal form identification, minimize risks of unexpected crystal forms, optimize drug formulations, and discover novel polymorphs with improved properties.

Variational AI is a company that uses generative AI to discover novel drug-like small molecules with optimized properties for defined targets. Their platform, Enki™, is the first commercially accessible foundation model for small molecules. It is designed to make generating novel molecule structures easy, with no data required. Users simply define their target product profile (TPP) and Enki does the rest. Enki is an ensemble of generative algorithms trained on decades worth of experimental data with proven results. The company was founded in September 2019 and is based in Vancouver, BC, Canada.

AI2BMD is a program for efficiently simulating protein molecular dynamics with ab initio accuracy. The repository contains datasets, simulation programs, and public materials related to AI2BMD. It provides a Docker image for easy deployment and a standalone launcher program. Users can run simulations by downloading the launcher script and specifying simulation parameters. The repository also includes ready-to-use protein structures for testing. AI2BMD is designed for x86-64 GNU/Linux systems with recommended hardware specifications. The related research includes model architectures like ViSNet, Geoformer, and fine-grained force metrics for MLFF. Citation information and contact details for the AI2BMD Team are provided.

NoLabs is an open-source biolab that provides easy access to state-of-the-art models for bio research. It supports various tasks, including drug discovery, protein analysis, and small molecule design. NoLabs aims to accelerate bio research by making inference models accessible to everyone.

AITom is an open-source platform for AI-driven cellular electron cryo-tomography analysis. It is developed to process large amounts of Cryo-ET data, reconstruct, detect, classify, recover, and spatially model different cellular components using state-of-the-art machine learning approaches. The platform aims to automate cellular structure discovery and provide new insights into molecular biology and medical applications.

The 'machine-learning-research' repository is a comprehensive collection of resources related to mathematics, machine learning, deep learning, artificial intelligence, data science, and various scientific fields. It includes materials such as courses, tutorials, books, podcasts, communities, online courses, papers, and dissertations. The repository covers topics ranging from fundamental math skills to advanced machine learning concepts, with a focus on applications in healthcare, genetics, computational biology, precision health, and AI in science. It serves as a valuable resource for individuals interested in learning and researching in the fields of machine learning and related disciplines.

Scientific Large Language Models (Sci-LLMs) is a repository that collects papers on scientific large language models, focusing on biology and chemistry domains. It includes textual, molecular, protein, and genomic languages, as well as multimodal language. The repository covers various large language models for tasks such as molecule property prediction, interaction prediction, protein sequence representation, protein sequence generation/design, DNA-protein interaction prediction, and RNA prediction. It also provides datasets and benchmarks for evaluating these models. The repository aims to facilitate research and development in the field of scientific language modeling.

Awesome-Segment-Anything is a powerful tool for segmenting and extracting information from various types of data. It provides a user-friendly interface to easily define segmentation rules and apply them to text, images, and other data formats. The tool supports both supervised and unsupervised segmentation methods, allowing users to customize the segmentation process based on their specific needs. With its versatile functionality and intuitive design, Awesome-Segment-Anything is ideal for data analysts, researchers, content creators, and anyone looking to efficiently extract valuable insights from complex datasets.

OpenCRISPR is a set of free and open gene editing systems designed by Profluent Bio. The OpenCRISPR-1 protein maintains the prototypical architecture of a Type II Cas9 nuclease but is hundreds of mutations away from SpCas9 or any other known natural CRISPR-associated protein. You can view OpenCRISPR-1 as a drop-in replacement for many protocols that need a cas9-like protein with an NGG PAM and you can even use it with canonical SpCas9 gRNAs. OpenCRISPR-1 can be fused in a deactivated or nickase format for next generation gene editing techniques like base, prime, or epigenome editing.

The Ersilia Model Hub is a unified platform of pre-trained AI/ML models dedicated to infectious and neglected disease research. It offers an open-source, low-code solution that provides seamless access to AI/ML models for drug discovery. Models housed in the hub come from two sources: published models from literature (with due third-party acknowledgment) and custom models developed by the Ersilia team or contributors.

AIDE is a machine learning code generation agent that can generate solutions for machine learning tasks from natural language descriptions. It has the following features: 1. **Instruct with Natural Language**: Describe your problem or additional requirements and expert insights, all in natural language. 2. **Deliver Solution in Source Code**: AIDE will generate Python scripts for the **tested** machine learning pipeline. Enjoy full transparency, reproducibility, and the freedom to further improve the source code! 3. **Iterative Optimization**: AIDE iteratively runs, debugs, evaluates, and improves the ML code, all by itself. 4. **Visualization**: We also provide tools to visualize the solution tree produced by AIDE for a better understanding of its experimentation process. This gives you insights not only about what works but also what doesn't. AIDE has been benchmarked on over 60 Kaggle data science competitions and has demonstrated impressive performance, surpassing 50% of Kaggle participants on average. It is particularly well-suited for tasks that require complex data preprocessing, feature engineering, and model selection.

REINVENT is a molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design, molecule optimization, and other small molecule design tasks. It uses a Reinforcement Learning (RL) algorithm to generate optimized molecules compliant with a user-defined property profile defined as a multi-component score. Transfer Learning (TL) can be used to create or pre-train a model that generates molecules closer to a set of input molecules.

MD-Agent is a LLM-agent based toolset for Molecular Dynamics. It uses Langchain and a collection of tools to set up and execute molecular dynamics simulations, particularly in OpenMM. The tool assists in environment setup, installation, and usage by providing detailed steps. It also requires API keys for certain functionalities, such as OpenAI and paper-qa for literature searches. Contributions to the project are welcome, with a detailed Contributor's Guide available for interested individuals.

AIMNet2 Calculator is a package that integrates the AIMNet2 neural network potential into simulation workflows, providing fast and reliable energy, force, and property calculations for molecules with diverse elements. It excels at modeling various systems, offers flexible interfaces for popular simulation packages, and supports long-range interactions using DSF or Ewald summation Coulomb models. The tool is designed for accurate and versatile molecular simulations, suitable for large molecules and periodic calculations.

The 'awesome-AI4MolConformation-MD' repository focuses on protein conformations and molecular dynamics using generative artificial intelligence and deep learning. It provides resources, reviews, datasets, packages, and tools related to AI-driven molecular dynamics simulations. The repository covers a wide range of topics such as neural networks potentials, force fields, AI engines/frameworks, trajectory analysis, visualization tools, and various AI-based models for protein conformational sampling. It serves as a comprehensive guide for researchers and practitioners interested in leveraging AI for studying molecular structures and dynamics.

AIRS is a collection of open-source software tools, datasets, and benchmarks focused on Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems. The goal is to develop and maintain an integrated, open, reproducible, and sustainable set of resources to advance the field of AI for Science. The current resources include tools for Quantum Mechanics, Density Functional Theory, Small Molecules, Protein Science, Materials Science, Molecular Interactions, and Partial Differential Equations.

A public repository collecting links to state-of-the-art training sets, QA, benchmarks and other evaluations for various ML and LLM applications in materials science and chemistry. It includes datasets related to chemistry, materials, multimodal data, and knowledge graphs in the field. The repository aims to provide resources for training and evaluating machine learning models in the materials science and chemistry domains.

GOLEM is an open-source AI framework focused on optimization and learning of structured graph-based models using meta-heuristic methods. It emphasizes the potential of meta-heuristics in complex problem spaces where gradient-based methods are not suitable, and the importance of structured models in various problem domains. The framework offers features like structured model optimization, metaheuristic methods, multi-objective optimization, constrained optimization, extensibility, interpretability, and reproducibility. It can be applied to optimization problems represented as directed graphs with defined fitness functions. GOLEM has applications in areas like AutoML, Bayesian network structure search, differential equation discovery, geometric design, and neural architecture search. The project structure includes packages for core functionalities, adapters, graph representation, optimizers, genetic algorithms, utilities, serialization, visualization, examples, and testing. Contributions are welcome, and the project is supported by ITMO University's Research Center Strong Artificial Intelligence in Industry.

This repository is dedicated to collecting and categorizing papers related to Retrieval-Augmented Generation (RAG) for AI-generated content. It serves as a survey repository based on the paper 'Retrieval-Augmented Generation for AI-Generated Content: A Survey'. The repository is continuously updated to keep up with the rapid growth in the field of RAG.

Assists in evaluating protein engineering tools.

Academic-level genomics expertise.

Genome Guide: Powered by OpenAI - A leader in genomic data analysis.

Echoes Watson & Crick, educates on DNA with depth.

I assist with statistical analysis for molecular biology

Research assistant for Atomic, Molecular, and Optics Physics

Professional chemistry assistant, SMILES/SMART supported molecule and reaction diagrams, and more!

A guide to electron configurations with a fun, cartoony approach.

生物化学领域的知识型助手，避免提供医学建议。

Script Examples and Resource Center for Helping with LAMMPS Input Generation and High-quality Tutorials (SERCHLIGHT)

A GPT that can provides lectures on Statistical Mechanics

A Beginners Guide to Quantum Magic