address PR review comments

Author: namiroues

index.md

@@ -7,13 +7,13 @@ title: MDAnalysis
 <img src="{{ site.baseurl }}/public/mdanalysis-logo_square.png"
 style="float: right" alt="MDAnalysis" width="30%"/>
 
-<!-- TODO: Correct link so it links to the specific section of this page [multiple formats]({{site.pypi.docs}}/documentation_pages/coordinates/init.html#id1)
- -->
-**MDAnalysis** is an open-source Python library for analyzing molecular dynamics (MD) trajectories across [multiple formats]({{site.pypi.docs}}/documentation_pages/coordinates/init.html#id1). It enables seamless reading and writing of simulation data, allowing users to efficiently analyze molecular structures and dynamics, including particle-based trajectories and individual coordinate frames (e.g., biomolecules in the [PDB format][]). 
+ The **MDAnalysis Project** develops open-source tools for the analysis of molecular simulation data, providing researchers with efficient and accessible solutions for studying molecular structures and dynamics. The project is a fiscally sponsored initiative of [NumFOCUS][], a nonprofit organization that supports open-source scientific computing.
+
+At the core of the project is MDAnalysis, **an open-source Python library** for analyzing molecular dynamics (MD) trajectories across [multiple formats]({{ site.docs.userguide.url }}/formats/index.html#formats). MDAnalysis enables seamless reading and writing of simulation data, allowing users to efficiently analyze molecular structures and dynamics, including particle-based trajectories and individual coordinate frames (e.g., biomolecules in the [PDB format][]).
 
-With MDAnalysis, you can access atomic coordinates as [NumPy][] arrays, providing a flexible and efficient framework for complex analysis tasks. The library includes powerful [atom selection commands]({{site.pypi.docs}}/documentation_pages/selections.html) for extracting subsets of structures, supports trajectory transformations (e.g., fitting to a reference structure), and can write out trajectories along with [atom selections]({{site.pypi.docs}}/documentation_pages/selections_modules.html#selection-exporters) in formats suitable for visualization or native analysis tools.
+With MDAnalysis, you can access atomic coordinates as [NumPy][] arrays, providing a flexible and efficient framework for complex analysis tasks. The library includes powerful [atom selection commands]({{ site.docs.userguide.url }}/selections.html) for extracting subsets of structures and supports trajectory transformations (e.g., fitting to a reference structure).
 
-Learn more about our **mission, development, team, and governance** on the [About MDAnalysis]({{ site.baseurl }}about/) page.
+Learn more about our **mission, development, team, and governance** on the [About MDAnalysis]({{ site.baseurl }}/about/) page.
 
 ## Get Started  
 
@@ -23,7 +23,7 @@ If you're new to MDAnalysis, explore the following resources to install the libr
 - [Learning MDAnalysis]({{ site.baseurl }}/pages/learning_MDAnalysis)  
 - [Documentation]({{ site.baseurl }}/pages/documentation)  
 
-## Community Hub
+## Community 
 
 MDAnalysis is driven by an active **community of users and contributors**. Stay updated and get involved through the following pages:  
 
@@ -44,14 +44,17 @@ Want to contribute to MDAnalysis? Here’s how:
 
 If you use MDAnalysis in your research, please cite it appropriately and consider displaying our MDAnalysis badge in your projects. All citation formats and badge instructions are available in our [Citation guidelines]({{ site.baseurl }}/pages/citations/).
 
-## Funding & Support
+Additionally, consider displaying our badge in your projects that use MDAnalysis. We provide several [embedding markup examples]({{ site.baseurl }}/pages/citations/#powered-by-mdanalysis).
 
-MDAnalysis has received generous support from organizations such as the **Chan Zuckerberg Initiative, Google, NumFOCUS, and the National Science Foundation**.  
+[![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org)
 
-To learn more about out Sponsors or how to support MDAnalysis, visit our [Funding]({{ site.baseurl }}/pages/funding/) page.
+## Funding & Support
 
+MDAnalysis is a fiscally sponsored project of [NumFOCUS][]. We have received generous support from organizations such as the **Chan Zuckerberg Initiative, Google, and the National Science Foundation**.
 
-[![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org)
+{{ site.numfocus.donate_button }}
+
+To learn more about our Sponsors or how to support MDAnalysis, visit our [Funding]({{ site.baseurl }}/pages/funding/) page.
 
 <a href="https://github.com/MDAnalysis/mdanalysis"><img style="position: absolute; top:
 0; right: 0; border: 0;"