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Redesigned Chemical Pages: Comprehensive Small Molecule Information in One Place

August 07, 2026

We’re pleased to announce the redesign of SGD’s chemical pages! These updated pages provide comprehensive information about small molecules relevant to yeast biology such as metabolites, drugs, and experimental compounds, all in a more accessible, more user-friendly format.

Why Chemical Information Matters

Small molecules play crucial roles in yeast biology, from essential metabolites that keep cells functioning to experimental compounds that reveal how cellular processes work. SGD chemical pages bring together curated information about how these chemicals affect yeast, connecting chemical entities to genes, phenotypes, and biological pathways.

What’s New?

Chemical Structures Front and Center

The redesigned pages now display interactive 2D chemical structures prominently at the top of each page. These structures clearly show molecular connectivity and functional groups, providing immediate visual recognition of the compound. No more hunting for the structure because it’s the first thing you see!

All Information on One Page

No need to navigate between multiple tabs! Everything you need to know about a chemical is now presented on a single, unified page:

Comprehensive Identifiers and Database Links:

This integration makes it easy to explore the chemical across multiple resources and access broader chemical and metabolic information.

Curated Experimental Data

Each chemical page now includes rich experimental data curated from the yeast literature:

Phenotype Annotations
See the effects of the chemical on yeast:

  • Growth effects
  • Metabolic changes
  • Other cellular processes

This section includes annotation statistics, top genes and phenotypes involving each chemical. Every phenotype annotation is linked to supporting experimental evidence and literature references, so you can trace findings back to the original research.

Gene Ontology Annotations and Enrichment

The GO Annotations section shows how the chemical is annotated within the Gene Ontology framework, connecting it to specific biological processes, molecular functions, and cellular components.

For metabolites, you’ll also find links to relevant metabolic pathways in YeastPathways throughout the GO annotation tables, connecting chemical entities to their biological context in small molecule metabolism.

The GO Enrichment section takes this further with statistical analysis showing which biological processes and molecular functions are significantly associated with genes affected by the chemical. This enrichment analysis helps you:

  • Understand the broader biological context of chemical-gene interactions
  • Identify patterns in how chemicals influence cellular systems
  • Generate hypotheses about mechanism of action

Shared Chemicals Network

Discover related compounds! The Shared Chemicals section displays other chemical entities that share similar properties, annotations, or biological roles. This network view makes it easy to:

  • Explore chemical families
  • Find compounds with similar effects
  • Identify potential alternative compounds for experiments

Complete Literature Coverage

The References section compiles all publications from which data about the chemical has been curated. This provides direct access to the primary literature and shows you the full scope of research on each compound.

Try It Out!

Explore the new chemical pages:

We Want Your Feedback!

These improvements are part of our ongoing commitment to making SGD more comprehensive and user-friendly. Have thoughts on the new chemical pages? Contact us at sgd-helpdesk@lists.stanford.edu.

Categories: Website changes

Tags: ChEBI, chemicals, GO enrichment, metabolites, phenotypes, redesign, user experience

Redesigned Protein Complex Pages: Enhanced Data Access and Improved User Experience

August 04, 2026

We’re excited to announce a comprehensive redesign of SGD’s macromolecular complex pages! We’ve overhauled these pages to make complex information more accessible, comprehensive, and easier to navigate.

Why Protein Complexes Matter

Protein complexes are fundamental functional units in cells that operate as groups of proteins that work together to carry out specific biological processes. Since 2019, SGD has provided detailed information about yeast protein complexes, including subunit composition, functions, interactions, and references. With this major redesign, we’ve made this critical information even more accessible and useful for researchers.

What’s New?

All Gene Ontology Information on One Page

One of the most significant improvements is the reorganization of Gene Ontology (GO) annotations. Previously, GO information was tucked away on a separate tab, requiring you to navigate away from the main view. Now, all GO annotations are prominently displayed right on the Summary page.

What you can see at a glance:

  • Molecular Function: What the complex does
  • Biological Process: What pathways or processes it participates in
  • Cellular Component: Where in the cell it’s located

No more tab-switching—everything you need is in one place!

GO-CAM Pathway Models for Complexes

We’ve also integrated GO-CAM (Gene Ontology Causal Activity Models) pathway models directly into complex pages. When available, these models appear below the GO annotations, showing how entire protein complexes fit into larger biological pathways and regulatory networks. This provides a systems-level view that complements the detailed subunit information available on individual gene pages.

Enhanced Composition Section

The new Composition section is packed with detailed subunit information:

Stoichiometry Data: For complexes where the subunit ratios have been experimentally determined, you’ll now see the exact stoichiometry. This quantitative information is crucial for understanding complex architecture.

Structural Information:

  • Expert-curated notes about complex assembly and structural features
  • Direct links to Protein Data Bank (PDB) entries for complexes with experimentally determined 3D structures
  • Protein-protein binding regions and interaction interfaces (when characterized)

Organized Display: Subunits are now grouped by their roles or relationships within the complex, making it easier to understand how the complex is organized.

Easy Navigation: Each subunit links directly to its SGD gene page, so you can quickly dive deeper into individual components.

Shared Biology Networks

Complex pages now include a Shared Biology section that shows:

  • GO annotations shared with other complexes
  • Subunits shared between complexes
  • Ranked lists that prioritize the most functionally related complexes

The ranking system helps you quickly identify the most relevant relationships and potential functional connections, making it easier to understand how different complexes relate to each other.

Improved User Experience Throughout

Beyond these major features, we’ve focused on overall usability:

  • Clearer section headers make information easy to find
  • Better spacing and organization improve readability
  • Consistent styling with other SGD page types provides a unified experience
  • Logical information hierarchy puts the most commonly accessed data front and center

Try It Out!

Explore the new complex pages:

We Want Your Feedback!

These improvements are based on feedback from the yeast research community, and we want to keep making SGD better. Have suggestions? Questions? Let us know at sgd-helpdesk@lists.stanford.edu.

Categories: Announcements, Website changes

Tags: Gene Ontology, GO annotations, GO-CAM, protein complexes, redesign, stoichiometry, UI, user experience, UX

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