Research teams lose an estimated 50% of their productive hours to fragmented workflows — toggling between a reference manager, a shared drive, a project tracker, and a messaging app just to keep a single study moving forward. If you have searched for Paperpile as a solution, you are not alone. It is one of the most popular reference managers in academia. But is it enough when your entire team needs to collaborate across multiple projects, track tasks, and connect knowledge across studies?
This comparison breaks down Paperpile and ScholarDock feature by feature, focusing on what matters most for collaborative research teams: reference management, project tracking, knowledge structuring, and day-to-day teamwork. By the end, you will know exactly which platform fits your team's workflow.
What is Paperpile?
Paperpile is a cloud-based reference management software built around the Google ecosystem. It lets researchers collect references from the web using a Chrome extension, organize PDFs in Google Drive, annotate papers, and insert citations directly into Google Docs and Microsoft Word.
Paperpile's core strength is its clean, minimal interface and tight integration with Google apps. For individual researchers who live in Chrome and Google Docs, it offers a smooth, low-friction workflow for saving papers and generating bibliographies. Team features include shared folders, shared libraries, and the ability to co-annotate PDFs.
Pricing starts at $2.99 per month (billed annually) for academic users, with business plans at $9.99 per month. Team subscriptions require per-seat licensing.
What is ScholarDock?
ScholarDock is a research project and reference management platform that combines three core functions into a single workspace: project management, reference management, and knowledge structuring.
Instead of handling only citations and PDFs, ScholarDock gives research teams a unified environment to manage entire studies from inception to publication. You can organize projects by topic, methodology, or publication stage. You can build structured reference libraries, tag and annotate sources, and create citation-ready bibliographies. And you can assign tasks, track progress across multiple studies, and collaborate with your team — all without switching tools.
ScholarDock also integrates AI to accelerate research-heavy tasks like extracting key findings from papers, suggesting related sources, summarizing literature, and automatically organizing references.
Paperpile vs ScholarDock at a glance
Paperpile is a dedicated reference manager with strong Google integration, ideal for individual researchers or small groups who primarily need citation and PDF management. ScholarDock is an all-in-one research workspace that adds project management, task tracking, and knowledge structuring on top of full reference management capabilities — built specifically for teams managing complex, multi-study workflows.
Reference management and citation tools
Both Paperpile and ScholarDock handle the fundamentals of reference management well — importing papers, organizing sources, and generating citations in standard formats like APA, MLA, Chicago, and thousands of journal-specific styles.
Paperpile's approach
Paperpile centers its workflow around the Chrome browser extension. You find a paper on Google Scholar, PubMed, or a publisher's site, click the extension, and the reference plus PDF are saved directly to your library in Google Drive. From there, you can organize with folders, labels, and stars. Duplicate detection and automatic metadata cleanup keep your library tidy.
For citations in Google Docs, Paperpile offers a sidebar plugin that lets you search your library and insert formatted citations without leaving your document. The Word plugin works similarly, though it has historically been less seamless than the Google Docs experience. Paperpile supports over 9,000 citation styles.
ScholarDock's approach
ScholarDock's reference library is built into the broader research workspace. You can import papers, tag and annotate sources, and create citation-ready bibliographies — but your references are also connected to the projects they belong to. This means you can see which sources are tied to which study, which team member added them, and how they relate to your project's timeline and milestones.
For teams managing multiple concurrent studies, this connected approach prevents the common problem of reference libraries becoming bloated and disorganized over time. Every source has context — not just metadata, but a clear link to the research it supports.
Verdict on reference management
For pure citation management, especially if your team lives in Google Docs, Paperpile is excellent. ScholarDock matches its core reference features while adding the project-level context that larger teams need to keep sources organized across studies.
Project management and task tracking
This is where the two platforms diverge most sharply. Paperpile does not offer any project management or task tracking features. It is a reference manager, and it stays within that scope.
Why this matters for teams
A 2018 study published in Nature found that the average research team has grown from 1.9 to 3.5 authors over the past five decades, with large-scale collaborations becoming increasingly common. Managing a team of researchers means coordinating who is doing what — literature searches, data collection, manuscript drafts, revisions, submissions — across overlapping timelines.
Without built-in project management, Paperpile users need a separate tool for this. Most teams end up combining Paperpile with Trello, Asana, Notion, or even spreadsheets to track project status. This creates the exact fragmentation problem that slows teams down: information about a study lives in three or four different apps, and no single view shows the full picture.
How ScholarDock solves this
ScholarDock lets you manage research projects from inception to publication inside the same workspace where your references live. You can:
Track project stages from grant proposal through data collection to manuscript submission
Assign tasks to team members and see who is working on what
Set deadlines and milestones for each phase of a study
Link references to specific project stages so you know which sources support which parts of your research
Monitor progress across multiple concurrent studies from a single dashboard
For a principal investigator managing a lab with five ongoing studies, or a postdoctoral researcher coordinating a systematic review with collaborators across institutions, this integration eliminates an entire layer of tool-switching overhead.
Team collaboration and shared workspaces
Paperpile's collaboration features
Paperpile offers three sharing mechanisms: quick links for sending individual papers, shared folders for project-level collaboration, and shared libraries for team-wide repositories. Team members need individual Paperpile subscriptions (managed through a team license), and each shared library maintains its own folders, labels, notes, and annotations.
This works well for sharing references and co-annotating PDFs. However, Paperpile's collaboration stops at the reference level. There is no shared project workspace, no team activity feed, no way to see what your collaborators are currently working on beyond the references they have added.
User reviews on platforms like Capterra and G2 consistently mention that while Paperpile's sharing works, it is "not as straightforward as it could be" for teams that need deeper collaboration beyond reference sharing.
ScholarDock's collaborative workspace
ScholarDock treats collaboration as a first-class feature across the entire research workflow, not just references. Teams get:
Shared project workspaces where every team member can see project notes, references, tasks, and timelines
Co-editing capabilities for project notes and documentation
Task assignment and accountability so every team member knows their responsibilities
Shared source collections with annotations visible to the whole team
Project dashboards that can be shared with advisors, collaborators, or review committees
The difference is scope. Paperpile collaborates at the reference library level. ScholarDock, a research project and reference management platform, collaborates at the entire research workflow level — from the first literature search to the final manuscript submission.
Knowledge structuring and cross-study connections
One of the most overlooked challenges in team-based research is knowledge fragmentation. Findings from one study often inform another. A methodology validated in one project could streamline a different one. But when each study's materials live in separate folders or separate tools, these connections get lost.
The folder-and-label approach
Paperpile organizes references using a traditional folder and label system. You can create nested folders, apply multiple labels to papers, and use stars for quick access. This is effective for individual researchers who maintain a personal taxonomy. But for teams working across studies, folders do not capture the relationships between sources, findings, and projects.
ScholarDock's connected knowledge model
ScholarDock lets you connect findings across papers, build conceptual maps, and maintain living literature reviews that evolve as your research progresses. You can link materials across projects so that a paper relevant to two different studies appears in both contexts without duplication.
For teams conducting systematic reviews or working in interdisciplinary fields, this is transformative. Instead of searching through folders to find "that paper from the other project," you can follow structured connections that show exactly how sources and findings relate across your team's entire body of work.
This approach aligns with FAIR data principles (Findable, Accessible, Interoperable, Reusable) — making research materials not just stored but genuinely discoverable and reusable across your team's projects.
Google Docs integration and citations in Google Docs
Paperpile's strongest feature is arguably its native Google Docs integration. The Chrome extension and Google Docs sidebar create a smooth citation workflow that many researchers swear by. If your team writes exclusively in Google Docs and your primary need is fast, reliable citations, Paperpile delivers.
ScholarDock also supports citation workflows, but its value proposition extends beyond any single writing tool. ScholarDock keeps your citations connected to the broader project context — so when you are building a bibliography, you are pulling from a library that is already organized by project, annotated by your team, and linked to your research milestones.
For teams that use a mix of writing tools — Google Docs for some drafts, Word for journal submissions, LaTeX for technical papers — ScholarDock's platform-agnostic approach offers more flexibility than Paperpile's Google-first model.
AI-powered research features
Paperpile's AI capabilities
Paperpile has introduced an "Ask AI" feature currently in private beta, which allows users to send content from PDFs to AI assistants like ChatGPT, Claude, Gemini, and NotebookLM. This is a useful bridge between your reference library and external AI tools, but it relies on third-party AI services rather than providing native AI-powered features within the reference management workflow.
ScholarDock's built-in AI
ScholarDock integrates AI directly into the research workflow. Its AI capabilities include:
Extracting key findings from papers automatically
Suggesting related sources you may have missed during literature searches
Summarizing literature for faster review and synthesis
Organizing and tagging references automatically based on content
Keeping research materials connected and discoverable from first search to final citation
Transcribing interviews and conducting surveys
For teams managing large volumes of literature — a systematic review might involve screening hundreds or thousands of papers — ScholarDock's native AI saves significant time. According to research from the University of Melbourne, researchers spend up to 40% of their working time on information retrieval and management tasks. AI that reduces this burden directly within your workflow, without requiring you to copy content into external tools, delivers compounding time savings.
Pricing and value for research teams
Paperpile
Academic plan: $2.99 per month per user (billed annually)
Business plan: $9.99 per month per user (billed annually)
Team subscriptions require per-seat licensing
Uses Google Drive for storage (subject to your Google storage limits)
30-day free trial with all features
For a team of five academic researchers, Paperpile costs roughly $180 per year. However, this only covers reference management. You still need separate tools (and potentially separate budgets) for project management, task tracking, and knowledge organization.
ScholarDock
ScholarDock bundles reference management, project management, and knowledge structuring into a single platform. For teams that would otherwise pay for Paperpile plus a project management tool plus a shared knowledge base, ScholarDock consolidates these costs into one subscription.
When evaluating total cost of ownership, consider not just the subscription price but the productivity cost of maintaining multiple disconnected tools. A team that spends even 30 minutes per day switching between apps and re-finding information loses over 120 hours per year — time that could be spent on actual research.
Which tool is better for research teams?
Choose Paperpile if your team's needs begin and end with reference management. If you work primarily in Google Docs, manage a single study at a time, and already have a project management solution you are happy with, Paperpile is a polished, affordable reference manager that does its job well.
Choose ScholarDock if your team manages multiple concurrent research projects and needs a connected workspace for references, project tracking, tasks, and knowledge structuring. If you are a principal investigator overseeing a lab, a research group leader coordinating multi-author publications, or a PhD candidate managing a complex thesis alongside collaborative projects, ScholarDock eliminates the tool fragmentation that slows teams down.
The core difference is not about which tool has better citation formatting or a cleaner PDF reader. It is about whether your team needs a reference manager or a research workflow platform. Paperpile is the former. ScholarDock is the latter.
If your research team is tired of scattered PDFs, disconnected project trackers, and citation workflows that exist in isolation from the rest of your work, ScholarDock brings your entire research workflow — sources, projects, and collaborators — into one connected workspace. It is the reference management software built for how modern research teams actually work.