Best Molecular Modeling Software in Japan

SYNTHIA™ Retrosynthesis software, developed by computer scientists and coded by chemists, allows scientists to quickly and easily navigate novel and innovative pathways for novel and previously published target molecules. You can quickly and efficiently scan hundreds pathways to identify the best options for your needs. Discover the most cost-effective route to your target molecule with the latest visualization and filtering features. You can easily customize the search parameters to eliminate or highlight reactions, reagents, or classes of molecules. Explore innovative and unique syntheses to build your desired molecule. Easy to generate a list for starting materials that are commercially available for your synthesis. ISO/IEC 27001 Information Security Certification will guarantee the confidentiality, integrity and protection of your data.

ChemDoodle 2D boasts a plethora of features tailored for chemistry, enabling you to create high-quality graphics while significantly reducing your workload. We dedicate considerable time to analyzing the visual output generated by ChemDoodle. The software intelligently arranges bonds in the appropriate orientations, unifies bond strokes, optimizes the placement of attributes, and makes insightful choices that result in stunning and attractive visuals. However, you always have the option to adjust settings according to your tastes. Each element of the graphic can be tailored to your specifications, allowing you to modify bond widths, arrowhead dimensions, as well as the transparency and color of shapes. The drawing controls in ChemDoodle are designed to effectively represent the atoms and bonds they depict. Ample visual feedback is readily available, and a variety of options for personalizing the drawing tools accommodate individual preferences, including those related to accessibility. Ultimately, ChemDoodle empowers you to create visuals that meet both your aesthetic desires and functional needs.

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.

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.

ArgusLab is a program designed for molecular modeling, graphics, and drug design, specifically for Windows platforms. While it may be somewhat outdated, it continues to enjoy a surprising level of popularity with over 20,000 downloads recorded. This software is available under a free license, which means you don't have to fill out any forms to access it. Educators can utilize as many copies as necessary for their classes, allowing students to benefit from ArgusLab’s features. However, it is important to note that redistributing ArgusLab from external websites is prohibited, although linking to the official site from your own is permitted. Currently, there is a modest initiative in progress to adapt ArgusLab for use on the iPad. Additionally, efforts have been made to integrate the Qt cross-platform development environment to potentially expand compatibility across Mac, PC, and Linux systems, enhancing its accessibility for a wider audience. This commitment to adaptability underscores the software's ongoing relevance in the field of molecular modeling.

PyMOL is a molecular visualization system that operates on a user-sponsored, open-source basis, with oversight and distribution managed by Schrödinger. The PyQt interface has replaced Tcl/Tk and MacPyMOL across all platforms, enhancing the user experience significantly. This software offers improved support for third-party plugins and custom scripting, making it a comprehensive tool for rendering and animating three-dimensional structures. Additionally, it includes a plug-in that allows users to incorporate 3D images and animations directly into PowerPoint presentations. Although PyMOL is a commercial product, the majority of its source code is accessible for free under a permissive license. This open-source initiative is sustained by Schrödinger and primarily funded through the sales of PyMOL licenses. Users benefit from open access to executables and a flexible evaluation policy. Recent updates feature an improved fuse command that prevents hypervalent bonds and replaces them with monovalent atoms instead, along with a properties inspector that now allows users to unset settings using the “delete” key. Furthermore, issues regarding the workspace disappearing at certain display resolutions have also been resolved, contributing to a more seamless experience for users.

Ascalaph Designer serves as a versatile tool for conducting molecular dynamic simulations. It integrates various implementations of molecular dynamics alongside methods from classical and quantum mechanics within a unified graphical interface. Users can optimize molecular geometries utilizing conjugate gradient techniques. The program displays molecular structures in distinct windows, each equipped with two cameras that facilitate simultaneous visualization from multiple angles and different graphic representations. To open a subwindow, users can adjust the splitter located in the corner of each graphical window. A simple click on an atom or bond with the left mouse button alters their color slightly, while a brief description of the selected object appears in the status bar. The wire-frame visualization is particularly effective for large molecules, such as proteins, due to its speed and efficiency. Additionally, the CPK wire frame style merges characteristics from the various styles mentioned earlier, enhancing user experience. This flexibility makes Ascalaph Designer an essential resource for researchers in molecular dynamics.

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.

StarDrop™, a comprehensive suite of integrated software, delivers the best in silico technology within a highly visual interface. StarDrop™, which allows seamless flow between the latest data, predictive modeling, and decision-making regarding the next round or synthesis, improves the speed, efficiency and productivity of the discovery process. A balance of different properties is essential for successful compounds. StarDrop™, which guides you through the multi-parameter optimization challenge, helps you target compounds with the highest chance of success. It also saves you time and resources by allowing you to synthesize fewer compounds and test them less often.

An integrated platform that bridges scientific reasoning, compound development, and computational tools is now available. Chemaxon’s Design Hub supports medicinal chemistry by facilitating the analysis and prioritization of innovative ideas. This unified platform allows users to design compounds and manage concepts seamlessly. Transitioning from traditional PowerPoint presentations to dynamic, visually engaging, and chemically searchable hypotheses enhances the compound design workflow. Users can conveniently utilize established physicochemical properties, computational models, novelty considerations, or accessible compound catalogs within an interactive visual setting. Collaborate with your Contract Research Organizations (CROs) in the compound development journey through this secure online resource. Furthermore, assess the gathered data from biological assays or experimental structural insights to derive Structure-Activity Relationships (SAR) and generate fresh hypotheses for subsequent optimization cycles. Your scientific ideas can be conveniently organized in a “designer's electronic lab notebook,” which features chemically aware drawing tools that streamline the design process. This comprehensive approach ensures that every step of compound development is efficient and well-documented, paving the way for future innovations.

Effortlessly create and share chemical structures using our online chemistry editor. Marvin Pro is a versatile drawing application that merges our advanced chemical intelligence with an intuitive interface. This tool empowers chemists, researchers, and students to quickly translate their ideas into visually appealing representations. With the capability to manage a multitude of objects, chemical structures, arrows, and text on a single canvas, Marvin Pro ensures precise alignment for all elements. Chemical editors should be user-friendly, and our solution makes it easy to visualize your chemical concepts clearly. The caliber of your drawings should reflect the dedication you invest in your research, and Marvin Pro enables you to produce high-quality visuals suitable for professional presentations. Let the canvas of Marvin Pro serve as an extension of your creativity, where you can incorporate predefined templates, color your structures, and include images from external sources. Additionally, you have the option to showcase the chemical formula alongside your structures, enhancing your visual communication even further. Whether you're drafting for a project or preparing for a presentation, Marvin Pro is designed to meet all your chemical visualization needs.

MoluCAD is a comprehensive molecular modeling and visualization application specifically designed for Windows users. This tool emerged from a three-year research initiative funded by the National Institutes of Health, which focused on developing affordable educational software tailored for chemistry students. In its most recent iteration, MoluCAD includes numerous sophisticated features typically reserved for high-end modeling software found on expensive workstations. The application is characterized by its user-friendly interface, high-quality graphics, and strong computational capabilities. Even those who are new to molecular modeling can effortlessly create models, examine them from various angles, produce animations of chemical reactions, and store all related data on their devices. Additionally, MoluCAD serves as an invaluable resource for academic institutions looking to enhance their chemistry curriculum with accessible technology.

MolPad seamlessly incorporates an interactive chemistry sketching tool into various online educational platforms. It allows educators to create open-ended questions regarding molecular structures and organic chemistry that extend beyond simply identifying correct answers. Explore how MolPad enhances online chemistry instruction through a low-code framework that facilitates the development of engaging content and intelligent assessments. Our platform has introduced multiple solutions for the intuitive drawing of structural formulas, allowing students to engage with concepts such as chemical nomenclature, functional groups, and Lewis structures in a digital setting. By offering targeted feedback based on individual mistakes, students can achieve a deeper understanding compared to traditional multiple-choice formats, ultimately fostering a richer learning experience in chemistry. Additionally, this interactive approach encourages students to think critically and creatively about chemical concepts.

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.

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.

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.

BIOVIA solutions establish a peerless environment for scientific management, enabling organizations rooted in science to forge and integrate innovations in biology, chemistry, and materials to enhance our quality of life. The distinguished BIOVIA portfolio emphasizes the seamless integration of diverse scientific disciplines, experimental methodologies, and information needs throughout the entire spectrum of research, development, QA/QC, and manufacturing processes. Its extensive capabilities encompass areas such as Scientific Informatics, Molecular Modeling/Simulation, Data Science, Laboratory Informatics, Formulation Design, BioPharma Quality & Compliance, and Manufacturing Analytics. Dedicated to fostering and accelerating innovation, BIOVIA aims to boost productivity, elevate quality standards, ensure compliance, minimize costs, and hasten product development across a variety of industries. By effectively managing and connecting scientific innovation processes and information, BIOVIA enhances collaboration throughout the entire product lifecycle, ultimately driving progress and advancement in scientific research and application.

The biopharmaceutical sector today is characterized by its intricate nature, driven by increasing demands for enhanced specificity and safety, the emergence of new treatment modalities, and a deeper understanding of complex disease mechanisms. To navigate this intricate landscape, a thorough grasp of therapeutic behavior is essential. Modeling and simulation techniques serve as a powerful method to investigate biological and physicochemical phenomena at the atomic scale, which can inform experimental work and expedite both discovery and development timelines. BIOVIA Discovery Studio consolidates over three decades of rigorously validated research alongside cutting-edge in silico methodologies, including molecular mechanics, free energy assessments, and the development of biotherapeutics, all within a unified platform. This comprehensive toolkit empowers researchers to delve into the subtleties of protein chemistry, facilitating the discovery and optimization of both small and large molecule therapeutics from the identification of targets through to lead optimization, thereby enhancing the overall efficiency of the drug development process. In an era where precision medicine is increasingly pivotal, such tools are indispensable for advancing therapeutic innovation.

Chemical Computing Group (CCG) is well-known for its dedication to collaborative scientific assistance. Operating from locations across North America, Europe, and Asia, our team, comprised of PhD-level scientists, partners closely with clients to deliver personalized support, practical training, and expert scientific guidance on a diverse array of projects. In addition to this, CCG is committed to the ongoing development of innovative technologies, leveraging the expertise of mathematicians, scientists, and software engineers while also engaging in scientific partnerships with our customers to enhance research outcomes. This collaborative approach not only improves client satisfaction but also fosters a culture of innovation within the organization.

ChemOffice significantly boosts the efficiency of scientists by providing tools that allow them to systematically organize and investigate their compounds, reactions, and relevant properties, transforming raw data into valuable insights that facilitate more informed decision-making. Additionally, ChemDraw for Excel integrates chemical data into Excel, empowering chemists to leverage Excel's analytical capabilities to sort, organize, and enrich their compound datasets while investigating structure-activity relationships. Meanwhile, Chem3D allows chemists to create three-dimensional models of their compounds, enabling them to examine the spatial arrangement and properties of these molecules to optimize their efficacy or selectivity. Furthermore, ChemFinder functions as an intelligent personal database, assisting scientists in managing their compound collections and enabling them to search and correlate chemical structures with their properties effectively. This comprehensive suite of tools collectively streamlines the workflow for researchers, enhancing their ability to conduct high-quality scientific work.

Avogadro serves as a sophisticated molecular editor and visualizer that caters to users across multiple platforms, making it ideal for fields such as computational chemistry, molecular modeling, bioinformatics, and materials science. The software boasts high-quality rendering capabilities and incorporates a robust plugin architecture, enhancing its functionality. As a free and open-source tool, Avogadro is compatible with Mac, Windows, and Linux operating systems, providing versatility for researchers and professionals in various scientific domains. Its design not only facilitates advanced molecular editing but also fosters collaboration and innovation within the scientific community.

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.

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.

To reduce attrition rates for molecular entities that are unlikely succeed in nomination as drug candidates, direct new compound synthesizers, and focus animal testing requirements, calculate drug toxicity and safety.

Expert algorithms can help you to understand complex structures using experimental data.