Best Drug Discovery Software for Startups - Page 2
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Compare the Top Drug Discovery Software for Startups as of December 2025 - Page 2
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Genedata Biologics
Genedata
Genedata Biologics® streamlines discovery of biotherapeutics including bispecifics, ADCs, TCRs, CAR-Ts, and AAVs. The most widely adopted platform across the industry, it integrates all discovery workflows so you can focus on true innovation. Accelerate research with a first-in-class platform uniquely designed from the start to digitalize biotherapeutic discovery. The platform facilitates complex R&D processes by designing, tracking, testing, and assessing novel biotherapeutics drugs. It works with any format, from antibodies, bi- or multi-specifics, ADCs, novel scaffolds, and therapeutic proteins, to engineered therapeutic cell lines such as TCRs and CAR-T cells. Acting as a central end-to-end data backbone, Genedata Biologics integrates all R&D processes, from library design and immunizations, selections and panning, molecular biology, screening, protein engineering, expression, purification, and protein analytics, to candidate developability and manufacturability assessments. -
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SCIEX
SCIEX
When operating LC-MS/MS for research or routine workflows, you expect to achieve fast, accurate, and conclusive results. The SCIEX software suite helps you get the most out of your high-performance LC-MS/MS system. It includes specific workflow and application modules to supplement your operating system. As a result, your mass spectrometer runs with the ideal software combination, tailored to your needs. These are the core engines of SCIEX nominal mass and accurate mass LC-MS/MS systems. They are for rapid and reliable data acquisition, processing, and reporting, all with compliance readiness. Combine high performance and simplicity with add-on modules for optimized quantitative and qualitative workflows. Translate your data into conclusive results even faster with application-specific software modules. -
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SILCS
SilcsBio
Site-Identification by Ligand Competitive Saturation (SILCS) generates 3D maps (FragMaps) of interaction patterns for chemical functional groups with your target molecule. Site-Identification by Ligand Competitive Saturation (SILCS) generates 3D maps (FragMaps) of interaction patterns for chemical functional groups with your target molecule. SILCS reveals intricacies of dynamics and provides tools to optimize ligand scaffolds using qualitative and quantitative binding pockets insights allowing more rapid and effective drug design. SILCS uses multiple small molecule probes with various functional groups, explicit solvent modeling, and target molecule flexibility to perform protein target mapping. Visualize favorable interactions with the target macromolecule. Gain insights to design better ligands with optimally placed functional groups. -
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StarDrop
Optibrium
With its comprehensive suite of integrated software, StarDrop™ delivers best-in-class in silico technologies within a highly visual and user-friendly interface. StarDrop™ enables a seamless flow from the latest data through predictive modeling to decision-making regarding the next round of synthesis and research, improving the speed, efficiency, and productivity of the discovery process. Successful compounds require a balance of many different properties. StarDrop™ guides you through this multi-parameter optimization challenge to target compounds with the best chance of success, saving you time and resources by enabling you to synthesize and test fewer compounds. -
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Simulations Plus
Simulations Plus
Our reputation as thought leaders in the areas of ADMET property prediction, physiologically-based pharmacokinetics (PBPK) modeling, pharmacometrics, and quantitative systems pharmacology/toxicology is earned through the success our clients have found through their relationship with us. We have the talent and 20+ years of experience to translate science into user-friendly software and provide expert consulting supporting drug discovery, clinical development research, and regulatory submissions. -
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AutoDock
AutoDock
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Over the years, it has been modified and improved to add new functionalities, and multiple engines have been developed. Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina. More recently, we developed AutoDock-GPU, an accelerated version of AutoDock4 that is hundreds of times faster than the original single-CPU docking code. AutoDock 4 actually consists of two main programs: autodock performs the docking of the ligand to a set of grids describing the target protein; autogrid pre-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualized. This can help, for example, to guide organic synthetic chemists design better binders. -
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metaphactory
metaphacts
metaphactory transforms your data into consumable, contextual & actionable knowledge and drives continuous decision intelligence. Out-of-the-box, intuitive interfaces for searching, browsing & exploring your Knowledge Graph. Low-code approach to building custom interfaces that enable business-user interaction with the Knowledge Graph. Start small, iterate often & add new use cases, new data and new users on the fly. Agile knowledge management & low-code platform for building applications. -
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Genomenon
Genomenon
Pharma companies need comprehensive genomic information to drive successful precision medicine programs, but decisions are often made using only a fraction of the data available, about 10%. Genomenon delivers 100% of the data. An efficient and cost-effective natural history research solution for pharma, ProdigyTM Patient Landscapes support the development of rare disease therapies by enhancing insights contained in retrospective and prospective health data. Using a powerful AI-driven approach, Genomenon delivers a comprehensive and expert assessment of every patient in the published medical literature, in a fraction of the time. Don’t miss anything, get insight into every genomic biomarker published in the medical literature. Every scientific assertion is supported by empirical evidence from the medical literature. Identify all genetic drivers and pinpoint which variants are known to be pathogenic according to ACMG clinical standards. -
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BioNeMo
NVIDIA
BioNeMo is an AI-powered drug discovery cloud service and framework built on NVIDIA NeMo Megatron for training and deploying large biomolecular transformer AI models at a supercomputing scale. The service includes pre-trained large language models (LLMs) and native support for common file formats for proteins, DNA, RNA, and chemistry, providing data loaders for SMILES for molecular structures and FASTA for amino acid and nucleotide sequences. The BioNeMo framework will also be available for download for running on your own infrastructure. ESM-1, based on Meta AI’s state-of-the-art ESM-1b, and ProtT5 are transformer-based protein language models that can be used to generate learned embeddings for tasks like protein structure and property prediction. OpenFold, a deep learning model for 3D structure prediction of novel protein sequences, will be available in BioNeMo service. -
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NVIDIA Clara
NVIDIA
Clara’s domain-specific tools, AI pre-trained models, and accelerated applications are enabling AI breakthroughs in numerous fields, including medical devices, imaging, drug discovery, and genomics. Explore the end-to-end pipeline of medical device development and deployment with the Holoscan platform. Build containerized AI apps with the Holoscan SDK and MONAI, and streamline deployment in next-generation AI devices with the NVIDIA IGX developer kits. The NVIDIA Holoscan SDK includes healthcare-specific acceleration libraries, pre-trained AI models, and reference applications for computational medical devices. -
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AIDDISON
Merck KGaA
AIDDISON™ drug discovery software combines the power of artificial intelligence (AI), machine learning (ML), and 3D computer-aided drug design (CADD) methods to act as a valuable toolkit for medicinal chemistry needs. As a unified platform for efficient and effective ligand-based and structure-based drug design, it integrates all the facets for virtual screening and supports methods for in-silico lead discovery and lead optimization. -
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Iktos
Iktos
Makya is the first user-friendly SaaS platform for AI-driven de novo drug design focused on Multi-Parametric Optimization (MPO). It enables the design of novel and easy-to-make compounds in line with a multi-objective blueprint with unprecedented speed, performance, and diversity. Makya offers multiple generative algorithms covering different use cases from hit discovery to lead optimization: fine-tuning generator to find optimal solutions within your chemical space in line with your project blueprint; novelty generator to find new ideas with high novelty for re-scaffolding/hit discovery; forward generator to design a focused library of compounds easily accessible from commercial starting materials. The new Makya 3D module enhances the user experience and scientific utility of Makya. With an extensive set of 3D modeling features in both ligand-based and structure-based pipelines, with Makya 3D you can now calculate 3D scores and use these to guide generations natively in Makya. -
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Metabolon
Metabolon
At Metabolon, we offer the largest Level 1 library in the metabolomics industry. Our proprietary library has been built and curated over 20 years and contains over 5,400 entries. The vast majority of entries in our library are Level 1 attributing approximately 85% (~4,600 entries); however, some are Level 2 (approximately 15% accounting for around 800 entries) due to a lack of commercial standards available to qualify for Level 1. Metabolon delivers accurate, highly actionable insights for our clients’ scientific or clinical inquiries due to our unmatched library breadth and industry-leading annotation confidence levels. Metabolomics applies to a wide range of research, from soil health to food nutrition and preclinical research to clinical trials. Whether you’re searching for trends in a group or refining an individual’s treatment, metabolomics can help you find answers to important questions. -
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Discngine Assay
Discngine
Discngine Assay is a laboratory informatics platform that integrates every phase of plate-based assays into a cohesive, compliant, and efficient workflow, making it an essential tool for screening research labs. It enables scientists to streamline the entire High Throughput Screening workflow, from sample management and assay data analysis to data warehousing and liquid handling equipment qualification. With its intuitive interface and robust API, Discngine Assay integrates seamlessly with Lab equipments and existing IT environment, ensuring efficient data capture and processing. Designed to accelerate new molecule discovery, it addresses the needs of pharmaceutical, biotech, and CRO industries, enhancing collaboration and driving innovation in life science research. -
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3decision
Discngine
3decision® is a cloud-based protein structure repository designed for comprehensive structural data management and advanced analytics, enabling small molecule and biologics discovery teams to accelerate structure-based drug design. It centralizes and standardizes experimental and in-silico protein structures from public sources like RCSB PDB and AlphaFoldDB, as well as proprietary data, supporting formats like PDBx/mmCIF and ModelCIF. This ensures easy access to X-Ray, NMR, cryo-EM, and modeled structures, fostering collaboration and enhancing research efforts. Beyond storage, 3decision® enriches entries with metadata and sequence information, including protein-ligand interactions, antibody annotations, and binding site details. Advanced analytical tools identify druggable sites, assess off-target risks, and enable binding site comparisons, transforming vast structural data into actionable knowledge. Its cloud-based platform facilitates collaboration among research teams. -
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Cytel
Cytel
Cytel is a leading global provider of clinical trial design software, biometric services, and advanced analytics, specializing in optimizing clinical trials and assisting pharmaceutical companies in unlocking the full potential of their clinical and real-world data. Founded in 1987 by distinguished statisticians Cyrus Mehta and Nitin Patel, Cytel has been at the forefront of adaptive clinical trial technology and biostatistical science. Our software solutions, including the East Horizon platform, empower precise trial design and simulation, utilizing adaptive and Bayesian tools to optimize protocols and accelerate drug development. The East Horizon platform integrates key components of Cytel's trusted software portfolio into a unified solution with R integration, enhancing trial design capabilities. Additionally, Cytel offers the Xact software suite, a comprehensive toolkit for statistical analyses of small datasets, and sparse, and missing data. -
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AQBioSim
SandboxAQ
AQBioSim is a cloud-native platform developed by SandboxAQ that leverages Large Quantitative Models (LQMs) grounded in physics and chemistry to revolutionize materials discovery and optimization. By integrating Density Functional Theory (DFT), Iterative Full Configuration Interaction (iFCI), Generative AI, Bayesian Optimization, and Chemical Foundation Models, AQBioSim enables high-fidelity simulations of molecular and material behaviors under real-world conditions. AQBioSim's capabilities include predicting performance under various stresses, accelerating formulation through in silico testing, and exploring sustainable chemical processes. Notably, AQBioSim has demonstrated significant advancements in battery technology by reducing lithium-ion battery end-of-life prediction time by 95%, achieving 35x greater accuracy with 50x less data. -
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Nautilus LIMS
Thermo Fisher Scientific
To accelerate new discoveries and get products to market as quickly as possible, R&D and manufacturing labs have to reconfigure and change on the fly. Data management can’t be a bottleneck. Developed in partnership with customers in fast-paced R&D environments, the Thermo Scientific™ Nautilus LIMS™ for Dynamic Discovery and R&D Environments is a highly flexible, easily configurable system that increases workflow efficiency, throughput and data reliability while simplifying administration, sample traceability and regulatory compliance. Automated handling of complex boards and proprietary graphics instruments make data monitoring and management easy, even novice users can delineate and track processes with ease. Clients can create workflows, delineate the life cycles of the samples and automate actions between different platforms while integrating regulated processes that comply with good laboratory practices and the 21 CFR Part 11 guidelines. -
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BioSymetrics
BioSymetrics
We integrate clinical and experimental data using machine learning to navigate human disease biology and advance precision medicines. Our patent-pending Contingent AI™ understands relationships within the data to provide sophisticated insights. We address data bias by iterating on machine learning models based upon decisions made in the pre-processing and feature engineering stages. We leverage zebrafish, cellular and other phenotypic animal models to validate in silico predictions in vivo experiments and genetically modify them in vitro and in vivo, to improve translation. Using active learning and computer vision on validated models for cardiac, central nervous system and rare disorders, we rapidly incorporate new data into our machine learning models. -
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LiveDesign
Schrödinger
LiveDesign is an enterprise informatics platform that enables teams to rapidly advance drug discovery projects by collaborating, designing, experimenting, analyzing, tracking, and reporting in a centralized platform. Capture ideas alongside experimental and modeling data. Create and store new virtual compounds in a centralized database, evaluate through advanced models, and prioritize new designs. Integrate biological data and model results across federated corporate databases, apply sophisticated cheminformatics to analyze all data at once, and progress compounds faster. Drive predictions and designs using advanced physics-based methods paired with machine learning techniques to rapidly improve prediction accuracy. Work together with remote team members in real-time. Share ideas, test, revise, and advance chemical series without losing track of your work. -
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Evidex
Advera Health Analytics
Automated surveillance of any data source, fully integrated with a GVP IX compliant signal management platform. GVP-IX compliant signal management platform integrated within Evidex and ready to use off-the-shelf. Modernize and audit-proof your management processes without having to move back and forth between platforms and services. Unlock the value of your safety data. When you automate signal detection and management, you can focus not just on regulatory requirements, but on driving value for your organization. Identify safety signals from traditional sources like ICSR databases, FDA Adverse Event Reporting System (FAERS), VigiBase and clinical trial data. Include new data sources such as claims, EHR, and other unstructured data. Bring these pools of information together seamlessly to enhance signaling algorithms, make validations and assessment more efficient, and provide faster answers to drug safety questions. -
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Aurora Drug Discovery
Aurora Fine Chemicals
Aurora employs quantum mechanics, thermodynamics, and an advanced continuous water model for solvation effects to calculate ligand´s binding affinities. This approach differs dramatically from scoring functions that are commonly used for binding affinity predictions. By including the entropy and aqueous electrostatic contributions in to the calculations directly, Aurora algorithms produce much more accurate and robust values of binding free energies. Interaction of a ligand with a protein is characterized by the value of binding free energy. The free energy (F) is the thermodynamic quantity that is directly related to experimentally measurable value of inhibition constant (IC50) and depends on electrostatic, quantum, aqueous solvation forces, as well as on statistical properties of interacting molecules. There are two major contributing quantities leading to non-additivity in F: 1) the electrostatic and solvation energy and 2) the entropy. -
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DNAnexus Apollo
DNAnexus
DNAnexus Apollo™ accelerates precision drug discovery by unlocking the power of collaboration to draw critical insights from omics data. Precision drug discovery requires collecting and analyzing huge volumes of omics and clinical data. These datasets are incredibly rich resources, but most legacy and home-grown informatics tools can't cope with their size and complexity. Precision medicine programs can also be hampered by siloed data sources, underpowered collaboration tools, and the burden of complex and always changing regulatory and security requirements. DNAnexus Apollo™ supports precision drug discovery programs by empowering scientists and clinicians to explore and analyze omics and clinical data together, in a single environment, built on a robust, scalable cloud platform. Apollo lets them share data, tools, and analyses easily and securely with peers and collaborators everywhere - whether they're on another floor, or another continent. -
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Basesoft PharmaSuite
Basesoft
The software that will help you improve the safety, traceability, quality, agility and integration of your Pharmacotechnics and Medicines Manufacturing Unit. No two pharmacy services are the same, which is why we have divided PharmaSuite into functional modules that will help you manage the different units in the most efficient way. Management of the Pharmacotechnics and Drug Preparation unit (parenteral mixtures). Management of parenteral nutrition. -
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Chemical Computing Group
Chemical Computing Group
Chemical Computing Group (CCG) has a strong reputation for collaborative scientific support. With offices in North America, Europe and Asia, our team of PhD-level scientists works closely with our clients, providing support, hands-on training and scientific advice on a wide range of projects. CCG continuously develops new technologies with its team of mathematicians, scientists and software engineers and through scientific collaborations with customers. -
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Chemia
Laurus Infosystems
Chemia is a Browser-based & cloud-ready ELN platform. Chemia is conceived, designed and architected by scientists for scientists. A platform to drive, assign, manage and monitor all R&D activities and record capture from one dashboard. It enables you to automate your R&D set-up and make it a truly paperless operation. It saves time(approx. an hour saved per scientist) with Cross-functional collaboration; makes you audit-ready and manages data effectively. Quick retrieval, search, comparative study, and reconfigurability enable faster and appropriate decisions. An inventory management system that organizes, maintains and schedules relevant information for chemicals and equipment used inside the laboratory. A system that provides usage logs of equipment, maintenance logs and calibration logs, for effective management of labs and efficient working. A system that provides the protocol and adherence to it for compliance. -
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Gritstone
Gritstone bio
The first pillar of our immunotherapy is our understanding of antigens and neoantigens, and specifically which ones will be transcribed, translated, processed and presented on a cell surface by Human leukocyte antigen (HLA) molecules; and therefore will be visible to T cells. We accomplish this through the use of Gritstone EDGETM, our proprietary machine learning-based platform. Developing cancer immunotherapies that include tumor-specific neoantigens presents a challenge due to their nature – tumors typically have hundreds of mutations, but only a small percentage of those mutations result in true tumor-specific neoantigens that are. To address this challenge, we trained EDGE’s novel integrated neural network model architecture with millions of data points from hundreds of tumor and normal tissue samples from patients of various ancestries. -
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Healnet
Healx
Rare diseases are often not well studied and there is a limited understanding of many of the aspects necessary to support a drug discovery program. Our AI platform, Healnet, overcomes these challenges by analyzing millions of drug and disease data points to find novel connections that could be turned into new treatment opportunities. By applying frontier technologies across the discovery and development pipeline, we can run multiple stages in parallel and at scale. One disease, one target, one drug: it's an overly simple model, yet it's the one used by nearly all pharmaceutical companies. The next generation of drug discovery is AI-powered, parallel and hypothesis-free. Bringing together the key three drug discovery paradigms. -
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Kanteron
Kanteron Systems
Kanteron Platform ingested medical images, digital pathology slides, genomics sequences, and patient data from modalities, scanners, sequencers and databases, and provided a complete data toolkit to every team in hospital networks. Pharmacogenomics for adverse medication event prevention, and Precision Medicine application at the point of care: Incorporates sources of drug-gene interaction data that were previously only available in in accessible formats (e.g. tables in a PDF document), implementing the major Pharmacogenomic databases (like PharmGKB, CGI, DGIdb, OpenTargets...) Allows the user to refine their query to certain gene families, types of interactions, classes of drugs, etc. Flexible AI means you can choose the data set that best fits your use case, and apply it to your relevant medical images. -
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Cortellis
Clarivate
Unlock hidden insights in data using the Cortellis™ suite of life science intelligence solutions – so you can make better informed decisions along the entire R&D lifecycle. We’ve removed the hard work of finding, integrating, and analyzing data so you can focus on the critical decisions needed to get your products to market faster. Applying a unique depth, breadth and quality of data that is enriched with deep domain knowledge, industry understanding, and therapeutic expertise, Cortellis unlocks hidden insights to drive data-driven decisions that accelerate innovation. Get precise, actionable answers to your specific questions across the R&D lifecycle with the broadest and deepest sources of intelligence. Accelerate innovation with Cortellis as an indispensable part of your daily workflow.
