Alternatives to BioNeMo

HyperProtein is the latest offering from Hypercube, Inc., concentrating on the computational analysis of protein sequences. This innovative product not only examines one-dimensional sequences but also delves into the resulting three-dimensional structures of proteins. A key aspect of HyperProtein is its exploration of the intricate relationship between a protein's sequence and its structural form. In contrast to standalone software that targets specific functions like sequence alignment, HyperProtein combines a wide array of Bioinformatics and Molecular Modeling tools, providing a comprehensive approach to the science that begins with a protein sequence. By integrating these diverse tools, HyperProtein aims to enhance the understanding of protein functions and interactions at a molecular level, making it a valuable resource for researchers in the field.

3decision® serves as a cloud-based repository for protein structures, focusing on efficient management of structural data and offering sophisticated analytics to support teams involved in the discovery of small molecules and biologics, thereby expediting the process of structure-based drug design. The platform consolidates and standardizes both experimental and computational protein structures sourced from publicly available databases such as RCSB PDB and AlphaFoldDB, in addition to proprietary datasets, and accommodates formats like PDBx/mmCIF and ModelCIF. This comprehensive approach guarantees seamless access to a variety of structural formats including X-Ray, NMR, cryo-EM, and modeled structures, thereby promoting collaboration and bolstering research initiatives. In addition to its storage capabilities, 3decision® enhances each entry with valuable metadata and sequence information, which encompasses details on protein-ligand interactions, antibody annotations, and specifics about binding sites. Equipped with advanced analytical instruments, the platform is capable of pinpointing druggable sites, evaluating off-target risks, and facilitating comparisons of binding sites, which collectively transform extensive structural datasets into practical insights that can drive research forward. Furthermore, its cloud-based architecture fosters enhanced collaboration among research teams, making it easier for scientists to share findings and insights, ultimately leading to more innovative approaches in drug discovery and development.

LigPlot+ serves as the advanced iteration of the original LIGPLOT software, designed for the automatic creation of 2D diagrams depicting ligand-protein interactions. This tool features a user-friendly Java interface that enables users to edit plots effortlessly through simple mouse click-and-drag actions. Besides the improved interface, LigPlot+ introduces several significant upgrades compared to its predecessor. When analyzing two or more ligand-protein complexes that share notable similarities, the software can automatically present their interaction diagrams either overlayed or side by side, with conserved interactions prominently highlighted for easy identification. Additionally, the LigPlot+ suite integrates an enhanced version of the original DIMPLOT program, which is focused on visualizing protein-protein or domain-domain interactions. Users have the flexibility to choose the specific interface they are interested in, allowing DIMPLOT to produce a detailed diagram that illustrates the residue-residue interactions within that interface. For further clarity in interpretation, the residues from one interface can also be displayed in their sequential order, enhancing the overall usability and functionality of the program. This comprehensive approach makes LigPlot+ a valuable tool for researchers seeking to understand complex molecular interactions more intuitively.

Proteins, which are remarkably complex machines, play a crucial role not only in the biological functions of your body but also in every living organism's processes. They serve as the fundamental units of life. As of now, there are approximately 100 million identified proteins, with discoveries being made regularly. Each protein possesses a distinctive three-dimensional shape that is essential to its functionality and purpose. However, determining a protein's precise structure is often a costly and lengthy endeavor, resulting in an understanding of only a small percentage of the proteins recognized by science. Addressing this growing disparity and developing methods to predict the structures of millions of yet-to-be-discovered proteins could significantly advance our ability to combat diseases, expedite the discovery of new treatments, and potentially unveil the secrets of life's mechanisms. The implications of such advancements could transform both medicine and our understanding of biology.

Swiss-PdbViewer, also known as DeepView, is a software tool that offers an intuitive interface for the simultaneous analysis of multiple proteins. Users can superimpose these proteins to determine structural alignments and evaluate various critical components, such as active sites. The application simplifies the process of obtaining information on amino acid mutations, hydrogen bonds, angles, and atomic distances through its easy-to-navigate graphical and menu-driven interface. Developed by Nicolas Guex since 1994, Swiss-PdbViewer was originally closely integrated with SWISS-MODEL, an automated homology modeling server created by the Swiss Institute of Bioinformatics (SIB) within the Structural Bioinformatics Group at the Biozentrum in Basel. Over time, the SWISS-MODEL web interface has progressed significantly, allowing for direct use in advanced modeling tasks. As a result, the complexity of maintaining a direct connection with Swiss-PdbViewer has led to the discontinuation of support for that integration. This evolution reflects broader changes in bioinformatics tools and their capabilities.

Genedata Biologics® enhances the development of biotherapeutics, including bispecifics, ADCs, TCRs, CAR-Ts, and AAVs, providing a comprehensive solution for the industry. Recognized as the leading platform in the field, it seamlessly unifies all discovery workflows, allowing researchers to prioritize genuine innovation. By utilizing a pioneering platform that was purposefully created to digitalize the biotherapeutic discovery process, research can be accelerated significantly. The platform simplifies intricate R&D tasks by facilitating the design, tracking, testing, and evaluation of novel biotherapeutic drugs. It is compatible with various formats, such as antibodies, bi- or multi-specifics, ADCs, innovative scaffolds, and therapeutic proteins, as well as engineered therapeutic cell lines like TCRs and CAR-T cells. Functioning as a comprehensive end-to-end data backbone, Genedata Biologics connects all R&D processes, including library design, immunization, selection and panning, molecular biology, screening, protein engineering, expression, purification, and protein analytics, ultimately leading to thorough assessments of candidate developability and manufacturability. This holistic integration ensures that researchers can make informed decisions and push the boundaries of biotherapeutic innovation effectively.

Founded in 2000, VeraChem LLC aims to enhance the field of computer-aided drug discovery and molecular design by creating advanced computational chemistry techniques that merge innovative basic science with practical applications in research. A key aspect of the company's strategy for product development lies in delivering efficient, high-performance software solutions along with extensive user support. Among the current capabilities of VeraChem's software are predictions for protein-ligand and host-guest binding affinities, rapid and precise calculations of partial atomic charges for drug-like molecules, and the computation of energies and forces utilizing widely-used empirical force fields. Additionally, the software features automatic generation of alternate resonance forms for drug-like compounds, a robust conformational search enabled by the Tork algorithm, and the automatic identification of topological and three-dimensional molecular symmetries. The modular code base of VeraChem’s software packages allows for flexibility and adaptability in meeting diverse research needs, ensuring that users can leverage these tools effectively for their specific applications.

The biopharmaceutical sector today is characterized by its intricacy, driven by increasing demands for enhanced specificity and safety, the emergence of new treatment classes, and the complexity of disease mechanisms. To navigate this intricate landscape, a profound comprehension of therapeutic dynamics is essential. Advanced modeling and simulation techniques offer a distinctive approach to investigate biological and physicochemical phenomena at the atomic scale. This methodology not only informs physical experimentation but also expedites the drug discovery and development phases. BIOVIA Discovery Studio integrates more than three decades of peer-reviewed research with cutting-edge in silico methodologies, including molecular mechanics, free energy assessments, and biotherapeutics developability, all within a unified framework. By equipping researchers with a comprehensive suite of tools, it facilitates a deeper examination of protein chemistry, thereby accelerating the discovery of both small and large molecule therapeutics, from Target Identification all the way through to Lead Optimization. Ultimately, this synergy of research and technology underscores the vital role of innovative tools in transforming biopharmaceutical advancements.

Profluent's innovative platform transforms the field of protein design by seamlessly combining cutting-edge AI technology with its own experimental capabilities, allowing for the development of proteins that are either inspired by nature or entirely newly conceived. This comprehensive methodology provides precise, flexible, and scalable solutions to intricate biological problems, resulting in advancements that push the boundaries of protein functionality. Profluent's foundational models extend protein design beyond the constraints of traditional random approaches, enabling the simultaneous optimization of various characteristics, enhancing sequence diversity, and unlocking new functionalities. By venturing into unexplored protein territories, Profluent presents distinctive opportunities that surpass the limitations of natural or patented proteins, streamlining the process for partners to achieve commercial viability in a more cost-effective and accessible manner. Underpinning Profluent's capabilities is a strong dedication to scientific excellence, utilizing a wide range of datasets and advanced AI techniques to address complex challenges effectively. As a result, Profluent not only advances protein engineering but also sets a new standard in the industry, fostering innovative collaborations and breakthroughs.

Evo 2 represents a cutting-edge genomic foundation model that excels in making predictions and designing tasks related to DNA, RNA, and proteins. It employs an advanced deep learning architecture that allows for the modeling of biological sequences with single-nucleotide accuracy, achieving impressive scaling of both compute and memory resources as the context length increases. With a robust training of 40 billion parameters and a context length of 1 megabase, Evo 2 has analyzed over 9 trillion nucleotides sourced from a variety of eukaryotic and prokaryotic genomes. This extensive dataset facilitates Evo 2's ability to conduct zero-shot function predictions across various biological types, including DNA, RNA, and proteins, while also being capable of generating innovative sequences that maintain a plausible genomic structure. The model's versatility has been showcased through its effectiveness in designing operational CRISPR systems and in the identification of mutations that could lead to diseases in human genes. Furthermore, Evo 2 is available to the public on Arc's GitHub repository, and it is also incorporated into the NVIDIA BioNeMo framework, enhancing its accessibility for researchers and developers alike. Its integration into existing platforms signifies a major step forward for genomic modeling and analysis.

Eidogen-Sertanty's Target Informatics Platform (TIP) stands out as the pioneering structural informatics system and knowledgebase that empowers researchers to explore the druggable genome through a structural lens. By harnessing the burgeoning wealth of experimental protein structure data, TIP revolutionizes structure-based drug discovery, shifting it from a limited, low-throughput field to a dynamic and data-rich scientific discipline. It is specifically designed to connect the realms of bioinformatics and cheminformatics, providing drug discovery scientists with a repository of insights that are not only unique but also highly synergistic with the information available from traditional bio- and cheminformatics tools. The platform's innovative combination of structural data management with advanced target-to-lead calculation and analytical capabilities significantly enhances every phase of the drug discovery process. With TIP, researchers are better equipped to navigate the complexities of drug development and make informed decisions.

Promethium is an innovative platform for chemistry simulations that harnesses the power of GPUs to significantly speed up the development of drugs and materials by providing more efficient and precise quantum chemistry calculations. Specifically engineered for NVIDIA data center GPUs, such as the A100, it utilizes advanced QC Ware streaming algorithms to deliver remarkable computational speed and impressive power efficiency. This platform can perform density functional theory (DFT) calculations on molecular systems containing as many as 2,000 atoms, enabling researchers to conduct simulations of large molecular structures that traditional CPU-based ab initio methods cannot handle. For example, it can execute a single-point calculation for a protein with 2,056 atoms in just 14 hours using only one GPU. Promethium is equipped with a diverse array of functionalities, including single-point energy computations, geometry optimizations, conformer searches, torsion scans, reaction path optimizations, transition state optimizations, interaction energy evaluations, and relaxed potential energy surface explorations. Its capabilities make it a powerful tool for chemists looking to push the boundaries of molecular modeling and simulation. Ultimately, Promethium is set to transform the landscape of computational chemistry.

Aurora utilizes principles of quantum mechanics and thermodynamics alongside a sophisticated continuous water model to assess the solvation effects on ligand binding affinities. This methodology is significantly different from the traditional scoring functions typically employed for predicting binding affinities. By integrating entropy and aqueous electrostatic contributions directly into the computations, Aurora's algorithms yield far more precise and reliable binding free energy values. The interaction between a ligand and a protein is fundamentally defined by the binding free energy value. This free energy (F) serves as a thermodynamic measure that correlates directly with the experimentally determined inhibition constant (IC50), influenced by factors such as electrostatic interactions, quantum effects, aqueous solvation forces, and the statistical characteristics of the molecules involved. Non-additivity in F arises primarily from two key components: the electrostatic and solvation energy, and the entropy, which together contribute to the complexity of ligand-protein interactions. Understanding these contributions is essential for the accurate prediction of binding affinities in drug design and molecular biology.

Dotmatics is the global leader in R&D scientific software that connects science, data, and decision-making. More than 2 million scientists and 10,000 customers trust Dotmatics to accelerate research and help make the world a healthier, cleaner, and safer place to live.

QSimulate presents an array of quantum simulation platforms that harness the principles of quantum mechanics to address intricate, large-scale challenges in life sciences and materials science. The QSP Life platform introduces innovative quantum-enhanced techniques for drug discovery and optimization, facilitating pioneering quantum simulations of ligand-protein interactions that are relevant throughout the entire computational drug discovery journey. Meanwhile, the QUELO platform enables hybrid quantum/classical free energy calculations, empowering users to conduct relative free energy assessments via the free energy perturbation (FEP) method. Furthermore, QSimulate's advancements enable significant progress in quantum mechanics/molecular mechanics (QM/MM) simulations tailored for extensive protein modeling. In the realm of materials science, the QSP Materials platform opens up quantum mechanical simulations to a broader audience, allowing experimentalists to streamline complex workflows without requiring specialized expertise, ultimately fostering greater innovation in the field. This democratization of technology marks a pivotal shift in how researchers can approach and solve scientific problems.

AutoDock is a comprehensive suite comprising automated docking tools that aim to forecast the binding interactions of small molecules, like substrates or potential drugs, with a receptor that has a known three-dimensional structure. Over time, this toolset has undergone various modifications and enhancements to introduce new features, alongside the development of multiple computational engines. The software currently includes two main versions: AutoDock 4 and AutoDock Vina, each serving distinct purposes. Recently, the introduction of AutoDock-GPU has provided a significantly accelerated alternative to AutoDock4, achieving docking speeds that are remarkably hundreds of times faster than the original single-CPU version. AutoDock 4 is fundamentally made up of two core components: autodock, which executes the docking of the ligand onto a series of grids that represent the target protein, and autogrid, which is responsible for generating these grids ahead of time. These atomic affinity grids are not just useful for docking purposes; they can also be visualized to aid researchers, particularly organic synthetic chemists, in crafting more effective binding agents. This visualization capability can help streamline the process of drug design significantly.

Evo Designer is a cutting-edge tool created by the Arc Institute, harnessing the power of the Evo 2 genomic foundation model to aid in the generation and analysis of DNA sequences. Users can enter nucleotide sequences or select specific organisms, prompting the model to produce relevant DNA sequences tailored to their needs. This platform also offers detailed annotations of coding regions and provides 3D protein visualizations for prokaryotic sequences through ESMFold, enhancing the understanding of protein structures. In addition to these features, Evo Designer evaluates sequences by calculating their perplexity and per-nucleotide entropy, which helps researchers gauge the complexity and variability of the sequences they are working with. The Evo 2 model at the core of this tool has been trained on an impressive dataset of over 9 trillion nucleotides sourced from a wide variety of prokaryotic and eukaryotic genomes. Utilizing a sophisticated deep learning architecture, it models biological sequences with single-nucleotide precision and boasts a context window that can extend up to 1 million tokens, thereby ensuring high accuracy in sequence representation and analysis. This combination of features makes Evo Designer an invaluable resource for genetic research and exploration.

Site-Identification by Ligand Competitive Saturation (SILCS) produces three-dimensional maps, known as FragMaps, that illustrate how different chemical functional groups interact with a specific target molecule. By revealing the complexities of molecular dynamics, SILCS offers tools that enhance the optimization of ligand scaffolds through both qualitative and quantitative insights into binding pockets, thereby streamlining the drug design process. This approach employs a range of small molecule probes, each featuring diverse functional groups, alongside explicit solvent modeling and accommodating the flexibility of the target molecule to effectively map protein targets. Furthermore, the technique allows researchers to visualize advantageous interactions with the target macromolecule. With these insights, scientists can strategically design improved ligands with functional groups situated in optimal positions for enhanced efficacy. The innovative nature of SILCS represents a significant advancement in the field of medicinal chemistry.

FutureHouse is a nonprofit research organization dedicated to harnessing AI for the advancement of scientific discovery in biology and other intricate disciplines. This innovative lab boasts advanced AI agents that support researchers by speeding up various phases of the research process. Specifically, FutureHouse excels in extracting and summarizing data from scientific publications, demonstrating top-tier performance on assessments like the RAG-QA Arena's science benchmark. By utilizing an agentic methodology, it facilitates ongoing query refinement, re-ranking of language models, contextual summarization, and exploration of document citations to improve retrieval precision. In addition, FutureHouse provides a robust framework for training language agents on demanding scientific challenges, which empowers these agents to undertake tasks such as protein engineering, summarizing literature, and executing molecular cloning. To further validate its efficacy, the organization has developed the LAB-Bench benchmark, which measures language models against various biology research assignments, including information extraction and database retrieval, thus contributing to the broader scientific community. FutureHouse not only enhances research capabilities but also fosters collaboration among scientists and AI specialists to push the boundaries of knowledge.

NVIDIA NeMo LLM offers a streamlined approach to personalizing and utilizing large language models that are built on a variety of frameworks. Developers are empowered to implement enterprise AI solutions utilizing NeMo LLM across both private and public cloud environments. They can access Megatron 530B, which is among the largest language models available, via the cloud API or through the LLM service for hands-on experimentation. Users can tailor their selections from a range of NVIDIA or community-supported models that align with their AI application needs. By utilizing prompt learning techniques, they can enhance the quality of responses in just minutes to hours by supplying targeted context for particular use cases. Moreover, the NeMo LLM Service and the cloud API allow users to harness the capabilities of NVIDIA Megatron 530B, ensuring they have access to cutting-edge language processing technology. Additionally, the platform supports models specifically designed for drug discovery, available through both the cloud API and the NVIDIA BioNeMo framework, further expanding the potential applications of this innovative service.

Ascalaph Designer is a versatile software designed for conducting molecular dynamic simulations. It integrates various implementations of molecular dynamics alongside classical and quantum mechanics methodologies from widely-used programs within a unified graphical interface. The software includes molecular geometry optimization utilizing conjugate gradient techniques. Molecular models are displayed in distinct windows, each equipped with dual camera views that enable simultaneous visualization from multiple angles and in various graphic representations. Users can easily open additional subwindows by adjusting the splitter located in the corner of each graphical display. By clicking an atom or bond with the left mouse button, users can slightly alter its color, and relevant information about the selected object is presented in the status bar. The wire-frame visualization style proves especially effective for large molecules, such as proteins, ensuring rapid rendering. Additionally, the CPK wire frame style effectively merges characteristics from several other visualization options, enhancing user experience. This program not only facilitates complex simulations but also significantly improves the analysis of molecular structures through its innovative display features.

MEGA, which stands for Molecular Evolutionary Genetics Analysis, is an intuitive and highly capable software suite tailored for examining DNA and protein sequence information from various species and populations. It allows for both automated and manual alignment of sequences, the construction of phylogenetic trees, and the testing of evolutionary theories. The software employs an array of statistical approaches such as maximum likelihood, Bayesian inference, and ordinary least squares, making it indispensable for comparative sequence analysis and insights into molecular evolution. Additionally, MEGA includes sophisticated functionalities like real-time caption generation to clarify the findings and methodologies applied during analysis, alongside the maximum composite likelihood method for calculating evolutionary distances. The program is enhanced with powerful visual aids, including an alignment/trace editor and a tree explorer, while also supporting multi-threading to optimize processing efficiency. Furthermore, MEGA is compatible with several operating systems, such as Windows, Linux, and macOS, ensuring accessibility for a diverse user base. In summary, MEGA stands out as a comprehensive tool for researchers delving into the intricacies of molecular genetics.

YASARA is a versatile molecular graphics, modeling, and simulation software that was introduced in 1993 and is compatible with Windows, Linux, MacOS, and Android platforms, designed to simplify the process of obtaining answers to your scientific inquiries. Featuring a user-friendly interface and stunning photorealistic visuals, it also accommodates budget-friendly virtual reality headsets, shutter glasses, and autostereoscopic displays, fostering an immersive experience that allows users to concentrate on their objectives while minimizing distractions from the software itself. At the core of YASARA is PVL (Portable Vector Language), an innovative development framework that delivers performance capabilities that far exceed those of conventional applications. This advanced framework empowers users to visualize even the most complex protein structures and facilitates genuine interactive real-time simulations with precise force fields on standard computing systems, while also leveraging GPU capabilities when available. By enabling users to manipulate molecules actively and engage with dynamic models instead of just viewing static images, YASARA represents a significant advancement in molecular modeling technology. This dynamic interaction not only enhances the learning experience but also encourages deeper exploration of molecular behavior.

CryoTrackIMS is a comprehensive software solution tailored for various fields, including molecular biology, cell banking, cellular biology, clinical samples, biorepositories, biobanking, biochemistry, immunology, and protein laboratories, as well as high-throughput screening, quality assurance, IVF labs, and core facilities. Users can effortlessly design any box, plate, or pie layout by choosing from rows and columns or opting for a pie configuration, allowing their custom box to be generated in mere seconds for data input. Efficient inventory management of precious biological samples and specimens is essential for both fundamental research and the biotech industry. Managing extensive collections of diverse samples such as DNA, RNA, plasmids, clones, proteins, peptides, probes, antibodies, enzymes, specimens, tissues, and cell lines can often become a challenging and overwhelming endeavor that results in significant financial costs alongside frustration and wasted time. CryoTrack provides an all-encompassing solution specifically designed for laboratories within universities, clinics, biotechnology firms, and pharmaceutical organizations. This advanced software not only simplifies sample tracking but also significantly enhances lab efficiency and productivity. By streamlining the organization of critical biological materials, CryoTrackIMS empowers researchers to focus more on their experiments and less on administrative burdens.

The Protein Platform is made up of desktop software, web based software, hardware and 3rd party services. It also includes cloud infrastructure. The main component for Wild Game Processors is our self-updating, distributed Windows desktop application ProteinOS. This facilitates an efficient handling of customer orders. Our kiosks are made up of MiniPCs and POS Receipt Printers. They also include Thermal Label Printers and RFID. Mobile PC carts with an onboard UPS allow for use away from a power outlet. Each order is assigned an RFID tag that, when scanned by each station, brings up the required data. Automated and customizable customer invoices and notifications (SMS/Voice/Email) are available. Keep your business moving with quick views of the current demand, freezer capacity and pending orders.

Uncover biological markers, generate insights into the mechanisms of disease, identify novel pharmaceuticals, or detect variations in protein concentrations through a meticulously structured series of experiments. We have simplified the process of harnessing the potential of mass spectrometry and proteomics, enabling you to concentrate on the intricacies of biology and advance toward groundbreaking discoveries. Our automated and consistent workflow facilitates faster initiation and completion of experiments, granting you the authority and adaptability to make timely decisions. By prioritizing biological insights and fostering collaborative efforts, our scalable proteomics data processing system is designed for repeated use. We have delegated intensive and repetitive tasks to the cloud, ensuring a smooth and satisfying experience. Our sophisticated proteomics workflow effectively integrates numerous complex elements, allowing for the efficient analysis and processing of larger-scale experiments, ultimately enhancing the research journey. Thus, with our innovative approach, researchers can now delve deeper into the molecular landscape and achieve more significant breakthroughs than ever before.

Quattro Research GmbH comprises a diverse group of professionals, including scientists and IT experts. Our mission is to create cutting-edge products and solutions tailored for clients in the life sciences, pharmaceutical, and chemical sectors. We specialize in the integration and separation of databases and intellectual property during mergers and spin-offs. Additionally, we implement biological and chemical registration systems that accommodate intricate proteins while adhering to the HELM notation. Researchers engaged with antibodies, antibody-drug conjugates, large peptides, RNA molecules, and other biomolecules require specialized software solutions. To address this need, Quattro Research provides advanced tools for the registration and management of biomolecules, utilizing the open HELM Notation and Editor. Our commitment to innovation ensures that we meet the evolving demands of the industry effectively.

AQBioSim is an innovative cloud-based platform created by SandboxAQ that utilizes Large Quantitative Models (LQMs) based on principles of physics and chemistry to transform the processes of material discovery and optimization. By combining techniques such as Density Functional Theory (DFT), Iterative Full Configuration Interaction (iFCI), Generative AI, Bayesian Optimization, and Chemical Foundation Models, AQBioSim facilitates highly accurate simulations of molecular and material behaviors in real-world scenarios. Among its numerous features, AQBioSim can predict performance under various stressors, enhance formulation processes through in silico testing, and investigate eco-friendly chemical methods. A standout achievement of AQBioSim lies in its remarkable progress in battery technology, where it has cut the time needed for lithium-ion battery end-of-life predictions by an astonishing 95%, while also attaining 35 times greater accuracy using only 50 times less data. This platform thus not only accelerates material innovation but also significantly contributes to advancements in sustainable energy solutions.

Orbit BioSequence from Questel is an advanced tool for intellectual property (IP) intelligence, tailored to assist researchers, patent experts, and biotech firms in the thorough analysis and management of biological sequence data within the IP realm. This software presents a sophisticated framework for scrutinizing, analyzing, and keeping track of nucleotide and protein sequences identified in patent documents, thereby providing users with unprecedented access to vital sequence information that is essential for fostering innovation and conducting competitive assessments. With Orbit BioSequence, users can execute highly precise similarity and identity searches throughout international patent databases, empowering organizations to pinpoint existing patents, mitigate infringement risks, and discover potential licensing or collaboration opportunities. Furthermore, the software employs state-of-the-art search algorithms alongside meticulously curated datasets, guaranteeing both accuracy and relevance in the results. The comprehensive nature of this tool positions it as an invaluable resource in the evolving landscape of biotechnology and intellectual property management.

NVIDIA NeMo Megatron serves as a comprehensive framework designed for the training and deployment of large language models (LLMs) that can range from billions to trillions of parameters. As a integral component of the NVIDIA AI platform, it provides a streamlined, efficient, and cost-effective solution in a containerized format for constructing and deploying LLMs. Tailored for enterprise application development, the framework leverages cutting-edge technologies stemming from NVIDIA research and offers a complete workflow that automates distributed data processing, facilitates the training of large-scale custom models like GPT-3, T5, and multilingual T5 (mT5), and supports model deployment for large-scale inference. The process of utilizing LLMs becomes straightforward with the availability of validated recipes and predefined configurations that streamline both training and inference. Additionally, the hyperparameter optimization tool simplifies the customization of models by automatically exploring the optimal hyperparameter configurations, enhancing performance for training and inference across various distributed GPU cluster setups. This approach not only saves time but also ensures that users can achieve superior results with minimal effort.

IPA can also help analyze small-scale experiments that produce gene and chemical lists. IPA allows for targeted searches on genes, chemicals, and drugs. It also allows the creation of interactive models of experimental system. Data analysis and search capabilities allow for the understanding of the significance of data, targets, or candidate biomarkers within larger biological or chemical systems. The Ingenuity Knowledge Base contains highly structured, detail-rich chemical and biological findings that backs the software. Learn more about QIAGEN Ingenuity Pathway Analysis. Comparison Analysis determines which pathways, upstream regulators and diseases are most important. It can also be used to identify biological functions across time, doses, and other conditions.

The Megatron-Turing Natural Language Generation model (MT-NLG) stands out as the largest and most advanced monolithic transformer model for the English language, boasting an impressive 530 billion parameters. This 105-layer transformer architecture significantly enhances the capabilities of previous leading models, particularly in zero-shot, one-shot, and few-shot scenarios. It exhibits exceptional precision across a wide range of natural language processing tasks, including completion prediction, reading comprehension, commonsense reasoning, natural language inference, and word sense disambiguation. To foster further research on this groundbreaking English language model and to allow users to explore and utilize its potential in various language applications, NVIDIA has introduced an Early Access program for its managed API service dedicated to the MT-NLG model. This initiative aims to facilitate experimentation and innovation in the field of natural language processing.

Version 8.0 of PDQuest 2-D analysis software provides a robust and adaptable platform for conducting 2-D gel electrophoresis analysis. Users can opt for PDQuest Basic for straightforward 2-D gel evaluations or PDQuest Advanced to access the most cutting-edge features designed for in-depth expression proteomics research. Regardless of the version selected, the advanced analytical tools effectively highlight subtle variations across different 2-D gels. The software employs powerful auto-matching algorithms that ensure quick and precise gel matching with minimal manual effort. Furthermore, PDQuest's versatile annotation capabilities make it an invaluable asset for creating a centralized database, enabling a wide array of characterization data to be associated with each spot on a master gel image. Sharing and reviewing information related to identified proteins is made simple and efficient. Additionally, the software offers adaptable spot cutting configurations that enhance accuracy, throughput, and flexibility in protein identification trials, making it an essential tool for researchers in the field.

Efficiently address tissue heterogeneity and the intricacies of microenvironments using the GeoMx Digital Spatial Profiler (DSP), which stands out as the most versatile and powerful spatial multi-omic platform for examining both FFPE and fresh frozen tissue sections. Unique among spatial biology platforms, GeoMx allows for non-destructive profiling of RNA and protein expression across various tissue compartments and cell populations, supported by an automated and scalable workflow that seamlessly integrates with conventional histology staining. You can spatially profile the entire transcriptome along with over 570 protein targets, either separately or concurrently, utilizing sample inputs such as whole tissue sections, tissue microarrays (TMAs), or organoids. By choosing GeoMx DSP, you position yourself at the forefront of spatial biology for effective biomarker discovery and hypothesis validation. With the ability to determine the relevant boundaries, you can rely on biology-driven profiling that enables you to focus on the tissue microenvironments and cell types that hold the most significance for your research. This innovative approach ensures that your analyses are both comprehensive and tailored to the specific biological contexts of interest.

This repository showcases an implementation of model parallel autoregressive transformers utilizing GPUs, leveraging the capabilities of the DeepSpeed library. It serves as a record of EleutherAI's framework designed for training extensive language models on GPU architecture. Currently, it builds upon NVIDIA's Megatron Language Model, enhanced with advanced techniques from DeepSpeed alongside innovative optimizations. Our goal is to create a centralized hub for aggregating methodologies related to the training of large-scale autoregressive language models, thereby fostering accelerated research and development in the field of large-scale training. We believe that by providing these resources, we can significantly contribute to the progress of language model research.

Selecting the appropriate business management software for your protein or specialty food processing and distribution operation can prove to be a daunting task. Many software packages fall short of providing all the necessary features, while others may be prohibitively expensive or overly complicated to use. Whether your focus is on meat and protein processing that demands precise portion control and custom cutting capabilities, or you are a specialty food processor relying on bills of materials or recipes for various culinary techniques such as cooking, baking, frying, mixing, or assembling your products, Provisions equips you with essential tools that enhance efficiency, lower operational costs, and optimize profit margins. Our tailored software solutions are supported by a dedicated team of professionals who are committed to assisting you during the implementation process and beyond. We strive to ensure that your software operates seamlessly and continues to deliver value on a daily basis. Our commitment to your success is unwavering, as we understand the unique challenges within the food processing industry.

Generative AI is transforming nearly every sector by opening up vast new avenues for knowledge and creative professionals to tackle some of the most pressing issues of our time. NVIDIA is at the forefront of this transformation, providing a robust array of cloud services, pre-trained foundation models, and leading-edge frameworks, along with optimized inference engines and APIs, to integrate intelligence into enterprise applications seamlessly. The NVIDIA AI Foundations suite offers cloud services that enhance generative AI capabilities at the enterprise level, allowing for tailored solutions in diverse fields such as text processing (NVIDIA NeMo™), visual content creation (NVIDIA Picasso), and biological research (NVIDIA BioNeMo™). By leveraging the power of NeMo, Picasso, and BioNeMo through NVIDIA DGX™ Cloud, organizations can fully realize the potential of generative AI. This technology is not just limited to creative endeavors; it also finds applications in generating marketing content, crafting narratives, translating languages globally, and synthesizing information from various sources, such as news articles and meeting notes. By harnessing these advanced tools, businesses can foster innovation and stay ahead in an ever-evolving digital landscape.

MolView is an engaging, open-source web tool designed to enhance the realms of science and education! Primarily, it serves as a platform for visualizing data online. Users can explore various scientific databases, such as those containing compounds, proteins, and spectra, and interact with the information presented through dynamic visualizations enabled by WebGL and HTML5 technologies. The development of this web application relies on several JavaScript libraries and online services. Additionally, the Virtual Model Kit has played a pivotal role in inspiring the creation of this innovative project, pushing the boundaries of how scientific data can be represented and understood. Ultimately, MolView aims to make scientific exploration more accessible and enjoyable for everyone.

StrainControl allows you to organize strains, cell lines, proteins, plasmids, oligos, chemicals, inventories, and more with ease. You have the flexibility to tailor all field titles to suit the specific requirements of your laboratory. Managing lab items has never been simpler, so why not try our free version today to see how StrainControl can benefit both you and your colleagues? There’s no need to repeatedly request the same items, ensuring that your lab operates more efficiently than ever before. Additionally, you can share your StrainControl database with other lab members through your computer network, facilitating collaboration. With user management features, you can create different accounts to secure your database effectively. StrainControl is packed with functionalities designed to streamline every aspect of lab management. You can manage various components such as strains, cell lines, proteins, plasmids, oligos, chemicals, and inventories, while also sharing your database across a network. Customize your experience by renaming modules, columns, and text fields or hiding unused columns. Create user accounts with specific permissions (read/write/admin, etc.), and utilize user-friendly guides for importing or exporting data. Moreover, you can link essential files like protocols and images directly to your database, enhancing accessibility and organization. StrainControl truly revolutionizes lab management, making it easier than ever to keep everything in order.

ESMFold demonstrates how artificial intelligence can equip us with innovative instruments to explore the natural world, akin to the way the microscope revolutionized our perception by allowing us to observe the minute details of life. Through AI, we can gain a fresh perspective on the vast array of biological diversity, enhancing our comprehension of life sciences. A significant portion of AI research has been dedicated to enabling machines to interpret the world in a manner reminiscent of human understanding. However, the complex language of proteins remains largely inaccessible to humans and has proven challenging for even the most advanced computational systems. Nevertheless, AI holds the promise of unlocking this intricate language, facilitating our grasp of biological processes. Exploring AI within the realm of biology not only enriches our understanding of life sciences but also sheds light on the broader implications of artificial intelligence itself. Our research highlights the interconnectedness of various fields: the large language models powering advancements in machine translation, natural language processing, speech recognition, and image synthesis also possess the capability to assimilate profound insights about biological systems. This cross-disciplinary approach could pave the way for unprecedented discoveries in both AI and biology.

Revolutionize the fields of drug discovery and materials research through cutting-edge molecular modeling techniques. Our computational platform, grounded in physics, combines unique solutions for predictive modeling, data analysis, and collaboration, facilitating swift navigation of chemical space. This innovative platform is employed by leading industries globally, serving both drug discovery initiatives and materials science applications across various sectors including aerospace, energy, semiconductors, and electronic displays. It drives our internal drug discovery projects, overseeing processes from target identification through hit discovery and lead optimization. Additionally, it enhances our collaborative research efforts aimed at creating groundbreaking medicines to address significant public health challenges. With a dedicated team of over 150 Ph.D. scientists, we commit substantial resources to research and development. Our contributions to the scientific community include more than 400 peer-reviewed publications that validate the efficacy of our physics-based methodologies, and we remain at the forefront of advancing computational modeling techniques. We are steadfast in our mission to innovate and expand the possibilities within our field.

Mosaic is the most trusted sample management software for life science laboratories. Mosaic is trusted by a global customer base, from small biotech companies to large pharma companies. It tracks and manages every stage of the sample lifecycle. Keep a digital representation of all your samples and operational data, current and past. During every step of sample preparation, locations, amounts, and concentrations will be accurately recorded and audited according to 21 CFR Part 11 standards. Extensive, proven integrations with instruments or informatics platforms to support end-to-end research workflows. Validated requests are processed and automated fulfillment is performed. This ensures that there are no errors in delivery. From one scientist managing a small collection, to thousands of users managing hundreds of millions of samples, the operations can be automated. One system that can manage a variety of sample types including cell lines, compound libraries, proteins, nucleic acid, and many more.

Since its inception in 1985, ChemDraw® solutions have delivered exceptional features and integrations that allow users to swiftly convert their concepts and sketches into impressive publications. ChemOffice+ Cloud serves as a comprehensive suite for chemistry communication, transforming chemical illustrations into valuable knowledge by streamlining the management, reporting, and presentation of chemistry research. This powerful suite is specifically designed to enhance and expedite communication within the field of chemistry. Building upon the foundation of ChemDraw Professional, ChemOffice+ Cloud offers a wide range of advanced tools that support scientific inquiry and collaboration. The once tedious process of drafting reports for chemical research is now significantly more efficient thanks to ChemOffice+ Cloud. With its robust capabilities for searching, reusing, selecting, and organizing chemical structures and data, chemists can effortlessly create polished PowerPoint presentations and manuscripts, making their work more accessible and impactful. This transformation not only saves time but also elevates the overall quality of research dissemination in the scientific community.

Qwen-7B is the 7-billion parameter iteration of Alibaba Cloud's Qwen language model series, also known as Tongyi Qianwen. This large language model utilizes a Transformer architecture and has been pretrained on an extensive dataset comprising web texts, books, code, and more. Furthermore, we introduced Qwen-7B-Chat, an AI assistant that builds upon the pretrained Qwen-7B model and incorporates advanced alignment techniques. The Qwen-7B series boasts several notable features: It has been trained on a premium dataset, with over 2.2 trillion tokens sourced from a self-assembled collection of high-quality texts and codes across various domains, encompassing both general and specialized knowledge. Additionally, our model demonstrates exceptional performance, surpassing competitors of similar size on numerous benchmark datasets that assess capabilities in natural language understanding, mathematics, and coding tasks. This positions Qwen-7B as a leading choice in the realm of AI language models. Overall, its sophisticated training and robust design contribute to its impressive versatility and effectiveness.

Clara provides specialized tools and pre-trained AI models that are driving significant advancements across various sectors, such as healthcare technologies, medical imaging, pharmaceutical development, and genomic research. Delve into the comprehensive process of developing and implementing medical devices through the Holoscan platform. Create containerized AI applications using the Holoscan SDK in conjunction with MONAI, and enhance deployment efficiency in next-gen AI devices utilizing the NVIDIA IGX developer kits. Moreover, the NVIDIA Holoscan SDK is equipped with acceleration libraries tailored for healthcare, alongside pre-trained AI models and sample applications designed for computational medical devices. This combination of resources fosters innovation and efficiency, positioning developers to tackle complex challenges in the medical field.