LigPlot+ Description
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.
LigPlot+ Alternatives
SmartDraw makes professional drawings and diagrams accessible to everyone. Non-technical users can quickly create floor plans, while professionals get the precision and scale they require. With industry-leading floor planning tools and an intuitive interface for traditional diagramming like flowcharts and organizational charts, SmartDraw delivers enterprise-ready power without unnecessary complexity.
Key features:
- Large collection of symbols and templates
- Ability to create custom shapes
- Import PDFs, images, Google Maps, Visio files, Visio stencils
- Draw to any scale
- Enrich drawings with data
- Generate manifest and bills of materials
- Generate diagrams from data automatically like org charts, AWS, Azure, PI Boards, and more
- Use natural language text prompts to generate diagrams with AI
- Save files directly to OneDrive, SharePoint, or Google Drive, or other preferred provider
- Integrations with the Microsoft and Google enterprise stack plus Confluence and Jira
SmartDraw supports a wide range of industries and real-world use cases, helping teams plan, document, and communicate more effectively. Construction professionals use it to create scaled floor plans, site layouts, and electrical and plumbing drawings. Fire departments rely on it for fire pre-planning and incident documentation, while police departments use it for accident reconstruction and crime scene diagrams. IT teams build network diagrams and cloud architectures, HR leaders create organizational charts, and product managers map out processes and workflows. From physical layouts to business processes, SmartDraw provides a single platform that adapts to the needs of each role and industry.
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Highcharts, a Javascript-based charting library, makes it easy to add interactive charts and graphs to web or mobile projects of any size.
Highcharts is used by more than 80% of the 100 biggest companies in the world, as well as thousands of developers from a variety of industries, including finance, publishing, application development, and data science.
Highcharts is in active development since 2009. It remains a favorite among developers due to its robust feature set and ease-of-use documentation, accessibility features and vibrant community.
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Aurora Drug Discovery
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.
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3decision
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.
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Integrations
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Company Details
Company:
EMBL-EBI
Headquarters:
United Kingdom
Website:
www.ebi.ac.uk/thornton-srv/software/LigPlus/
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Product Details
Platforms
Windows
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Online Support
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