Best AI tools for< Computational Chemist >

XtalPi is a world-leading technology company driven by artificial intelligence (AI) and robotics to innovate in the fields of life sciences and new materials. Founded in 2015 at the Massachusetts Institute of Technology (MIT), the company is committed to realizing digital and intelligent innovation in the fields of life sciences and new materials. Based on cutting-edge technologies and capabilities such as quantum physics, artificial intelligence, cloud computing, and large-scale experimental robot clusters, the company provides innovative technologies, services, and products for global industries such as biomedicine, chemicals, new energy, and new materials.

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.

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.

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

Cradle is a protein engineering platform that uses machine learning to design improved protein sequences. It allows users to import assay data, generate new sequences, test them in the lab, and import the results to improve the model. Cradle can be used to optimize multiple properties of a protein simultaneously, and it has been used by leading biotech teams to accelerate new and ongoing projects.

The Institute for Protein Design is a research institute at the University of Washington that uses computational design to create new proteins that solve modern challenges in medicine, technology, and sustainability. The institute's research focuses on developing new protein therapeutics, vaccines, drug delivery systems, biological devices, self-assembling nanomaterials, and bioactive peptides. The institute also has a strong commitment to responsible AI development and has developed a set of principles to guide its use of AI in research.

Julius AI is an advanced AI data analyst tool that allows users to analyze data with computational AI, chat with files to get expert-level insights, create sleek data visualizations, perform modeling and predictive forecasting, solve math, physics, and chemistry problems, generate polished analyses and summaries, save time by automating data work, and unlock statistical modeling without complexity. It offers features like generating visualizations, asking data questions, effortless cleaning, instant data export, creating animations, and supercharging data analysis. Julius AI is loved by over 1,200,000 users worldwide and is designed to help knowledge workers make the most out of their data.

Artificial Intelligence: Foundations of Computational Agents, 3rd edition by David L. Poole and Alan K. Mackworth, Cambridge University Press 2023, is a book about the science of artificial intelligence (AI). It presents artificial intelligence as the study of the design of intelligent computational agents. The book is structured as a textbook, but it is accessible to a wide audience of professionals and researchers. In the last decades we have witnessed the emergence of artificial intelligence as a serious science and engineering discipline. This book provides an accessible synthesis of the field aimed at undergraduate and graduate students. It provides a coherent vision of the foundations of the field as it is today. It aims to provide that synthesis as an integrated science, in terms of a multi-dimensional design space that has been partially explored. As with any science worth its salt, artificial intelligence has a coherent, formal theory and a rambunctious experimental wing. The book balances theory and experiment, showing how to link them intimately together. It develops the science of AI together with its engineering applications.

Proscia is a leading provider of digital pathology solutions for the modern laboratory. Its flagship product, Concentriq, is an enterprise pathology platform that enables anatomic pathology laboratories to achieve 100% digitization and deliver faster, more precise results. Proscia also offers a range of AI applications that can be used to automate tasks, improve diagnostic accuracy, and accelerate research. The company's mission is to perfect cancer diagnosis with intelligent software that changes the way the world practices pathology.

Live Portrait Ai Generator is an AI application that transforms static portrait images into lifelike videos using advanced animation technology. Users can effortlessly animate their portraits, fine-tune animations, unleash artistic styles, and make memories move with text, music, and other elements. The tool offers a seamless stitching technology and retargeting capabilities to achieve perfect results. Live Portrait Ai enhances generation quality and generalization ability through a mixed image-video training strategy and network architecture upgrades.

Owkin is a full-stack AI biotech company that integrates the best of human and artificial intelligence to deliver better drugs and diagnostics at scale. By understanding complex biology through AI, Owkin identifies new treatments, de-risks and accelerates clinical trials, and builds diagnostic tools to reduce time to impact for patients.

NLTK (Natural Language Toolkit) is a leading platform for building Python programs to work with human language data. It provides easy-to-use interfaces to over 50 corpora and lexical resources such as WordNet, along with a suite of text processing libraries for classification, tokenization, stemming, tagging, parsing, and semantic reasoning, wrappers for industrial-strength NLP libraries, and an active discussion forum. Thanks to a hands-on guide introducing programming fundamentals alongside topics in computational linguistics, plus comprehensive API documentation, NLTK is suitable for linguists, engineers, students, educators, researchers, and industry users alike.

Bay Area AI is a technical AI meetup group based in San Francisco, CA, consisting of startup engineers, research scientists, computational linguists, mathematicians, and philosophers. The group focuses on understanding the meaning of text, reasoning, and human intent through technology to build new businesses and enhance the human experience in the modern connected world. They work on building systems with Machine Learning on top of Data Pipelines, exploring open-source solutions, and modeling human behavior in industry for practical results.

Wolfram is a comprehensive platform that unifies algorithms, data, notebooks, linguistics, and deployment to provide a powerful computation platform. It offers a range of products and services for various industries, including education, engineering, science, and technology. Wolfram is known for its revolutionary knowledge-based programming language, Wolfram Language, and its flagship product Wolfram|Alpha, a computational knowledge engine. The platform also includes Wolfram Cloud for cloud-based services, Wolfram Engine for software implementation, and Wolfram Data Framework for real-world data analysis.

Wolfram|Alpha is a computational knowledge engine that answers questions using data, algorithms, and artificial intelligence. It can perform calculations, generate graphs, and provide information on a wide range of topics, including mathematics, science, history, and culture. Wolfram|Alpha is used by students, researchers, and professionals around the world to solve problems, learn new things, and make informed decisions.

Altair is a global leader in computational intelligence, offering software and cloud solutions in simulation, HPC, data analytics, and AI. The platform provides advanced technology for accelerating AI adoption, powering engineering processes, and enabling sustainability solutions across various industries. Altair's products and platforms cater to diverse sectors such as aerospace, automotive, healthcare, and more, with a focus on digital twin technology, generative AI, and cloud computing. The company also hosts events, webinars, and training programs to support users in leveraging their tools effectively.

Spectre is an AI-powered shutter for iPhone that enables users to create amazing long exposures effortlessly. It simplifies the technical aspects of long exposures, such as camera stability and light estimation, making it accessible to all users. Spectre is designed by the team behind Halide, incorporating cutting-edge computational photography technologies like AI scene detection and intelligent exposure. The app is user-friendly, with a dark UI for night shooting and intuitive controls for a seamless experience. Spectre is not just a camera app but a showcase of high-tech features like DCI-P3 Wide Color Gamut and Machine Learning, setting it apart as a top camera application on the App Store.

Phenaki is a model capable of generating realistic videos from a sequence of textual prompts. It is particularly challenging to generate videos from text due to the computational cost, limited quantities of high-quality text-video data, and variable length of videos. To address these issues, Phenaki introduces a new causal model for learning video representation, which compresses the video to a small representation of discrete tokens. This tokenizer uses causal attention in time, which allows it to work with variable-length videos. To generate video tokens from text, Phenaki uses a bidirectional masked transformer conditioned on pre-computed text tokens. The generated video tokens are subsequently de-tokenized to create the actual video. To address data issues, Phenaki demonstrates how joint training on a large corpus of image-text pairs as well as a smaller number of video-text examples can result in generalization beyond what is available in the video datasets. Compared to previous video generation methods, Phenaki can generate arbitrarily long videos conditioned on a sequence of prompts (i.e., time-variable text or a story) in an open domain. To the best of our knowledge, this is the first time a paper studies generating videos from time-variable prompts. In addition, the proposed video encoder-decoder outperforms all per-frame baselines currently used in the literature in terms of spatio-temporal quality and the number of tokens per video.

Sacred is a tool to configure, organize, log and reproduce computational experiments. It is designed to introduce only minimal overhead, while encouraging modularity and configurability of experiments. The ability to conveniently make experiments configurable is at the heart of Sacred. If the parameters of an experiment are exposed in this way, it will help you to: keep track of all the parameters of your experiment easily run your experiment for different settings save configurations for individual runs in files or a database reproduce your results In Sacred we achieve this through the following main mechanisms: Config Scopes are functions with a @ex.config decorator, that turn all local variables into configuration entries. This helps to set up your configuration really easily. Those entries can then be used in captured functions via dependency injection. That way the system takes care of passing parameters around for you, which makes using your config values really easy. The command-line interface can be used to change the parameters, which makes it really easy to run your experiment with modified parameters. Observers log every information about your experiment and the configuration you used, and saves them for example to a Database. This helps to keep track of all your experiments. Automatic seeding helps controlling the randomness in your experiments, such that they stay reproducible.

The Open MatSci ML Toolkit is a flexible framework for machine learning in materials science. It provides a unified interface to a variety of materials science datasets, as well as a set of tools for data preprocessing, model training, and evaluation. The toolkit is designed to be easy to use for both beginners and experienced researchers, and it can be used to train models for a wide range of tasks, including property prediction, materials discovery, and materials design.

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.

AlphaFold3 is an implementation of the Alpha Fold 3 model in PyTorch for accurate structure prediction of biomolecular interactions. It includes modules for genetic diffusion and full model examples for forward pass computations. The tool allows users to generate random pair and single representations, operate on atomic coordinates, and perform structure predictions based on input tensors. The implementation also provides functionalities for training and evaluating the model.

This repository contains the code for the paper Fine-Tuned Language Models Generate Stable Inorganic Materials as Text. It demonstrates how finetuned LLMs can be used to generate stable materials, match or exceed the performance of domain specific models, mutate existing materials, and sample crystal structures conditioned on text descriptions. The method is distinct from CrystaLLM, which trains language models from scratch on CIF-formatted crystals.

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.

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.

ADMET-AI is a platform for ADMET prediction using Chemprop-RDKit models trained on ADMET datasets from the Therapeutics Data Commons. It offers command line, Python API, and web server interfaces for making ADMET predictions on new molecules. The platform can be easily installed using pip and supports GPU acceleration. It also provides options for processing TDC data, plotting results, and hosting a web server. ADMET-AI is a machine learning platform for evaluating large-scale chemical libraries.

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.

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.

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.

Expert in generating and explaining mathematical, chemical, and computational formulas.

A digital homage to honor Stephen Wolfram's impact on computational science and technology and to celebrate his dedication to public education, powered by Stephen Wolfram's wealth of public presentations, writings, and live streams.

Assists in evaluating protein engineering tools.

💡 Inventor of languages

Skilled in Python, Linux, R, and more.

AI protein design assistant

Expert in Marian NMT models and training

大型语言模型的学习和训练指导专家

Formal OpenMC Python API and debugging expert.

Blends academic insights & accessible explanations on P vs NP, drawing from Lance Fortnow's works.

A playful CFD advisor

Expert in OpenFOAM for CFD queries

Expert in GH-Python scripting & Grasshopper components

Advises on Bioconda recipes, following community guidelines

A interactive chatbot

Advanced AI for complex computations and data analysis.