Revilico product changelog and release notes

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New features

• Launched a CRO Directory in the admin panel, giving admins a centralized view of contract research organizations to accelerate quote and outreach workflows.
• Added a pipeline importer with drag-and-drop in Compound Review, letting you seed reviews directly from prior pipeline outputs without manual re-entry.
• Introduced a Resend Invite action so admins can re-send user invitations without recreating them.
• Added an admin result-download endpoint and a client outreach summary to streamline post-run reporting.

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Improvements

• Enhanced Compound Review with campaign tagging and like/dislike feedback on compounds, plus additional review workflow refinements.
• Added a right-hand-side panel for My Experiments and Admin Quote tickets so context stays visible while you work.
• Refreshed the sidebar with a minimize toggle for the Credit Usage widget and restricted the billing link to admins for cleaner navigation.
• Enforced a 1,000,000-credit cap on overage usage to protect accounts from runaway consumption.
• Streamlined the metered credit configuration by removing legacy pricing multipliers, producing more predictable billing behavior.
• Improved Adaptyv Bio integration UX: the platform now live-validates stored API keys and surfaces missing or invalid credentials with clearer 401/403 error messaging across all Adaptyv Bio pages.
• Improved batching behavior in Compound Review for large compound sets.

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Bug fixes

• Fixed the ⌘/Ctrl + [ shortcut so it now correctly collapses the left sidebar in classic navigation mode.
• Resolved a pose-loading issue in ensemble docking that could prevent results from rendering after a run.
• Fixed an issue where a feature flag was not applied correctly during pipeline execution.

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Metered Credit System

• Rolled out the Metered Credit System, moving from preview to full usage-based credit accounting for a clearer, fairer billing experience.
• Introduced Credit Bundles — prepaid and postpaid bundles to match usage patterns.
• Added a cap on overage credits to protect against unexpected usage spikes.
• Streamlined credit bundle options based on early user feedback.

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Compound Review

• Added Compare & Campaign to Compound Review — compare compounds side by side, with campaign tracking and like/dislike feedback.

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Platform

• Refreshed the sidebar interface for easier navigation.
• Delivered performance improvements across the platform.

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Billing

• Introduced the Metered Credit System (Preview), a refreshed credit experience ahead of full usage-based credits.
• Added Subscription Plan Controls to enable or disable subscription plans.

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Project Hub & Navigation

• Launched Project Hub Planning & Timeline — an interactive project timeline you can drag, resize, zoom, and jump to today.
• Added Classic Navigation Mode, letting users choose between classic (always-open) and compact side navigation.

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Collaboration

• Enhanced Team Chat with expanded Slack integration.

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Modeling & Data

• Expanded RevQSAR & MD Descriptor modeling and analysis support, with an updated interface.
• Added RevData Safeguards — checks when dropping data files into forms.
• Released a second set of Demo Pipelines for RevFEP, RevMut-PMX, and RevQS.

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Improvements & Changes

• Updated pipeline navigation to match new product routes.
• Enhanced the RevMD-Bind protein-ligand pipeline.
• Enhanced report generation.
• Delivered overall performance and responsiveness improvements across pipelines.

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RevFEP — Cloud-Native Free Energy Perturbation

• Launched RevFEP, a cloud-native Free Energy Perturbation engine for binding affinity prediction powered by OpenFE 1.10, OpenMM, and AWS Batch GPU execution.
• Added support for four calculation types: RBFE (relative binding free energy), ABFE (absolute binding free energy), and complementary protocols for lead-optimization ranking.
• Implemented seven advanced protocol stages including non-equilibrium MD, REST2 enhanced sampling, adaptive lambda optimization, and MM-GBSA pre-filtering.
• Automated the full pipeline from raw protein–ligand complex PDB inputs through structure preprocessing, alchemical network construction, GPU simulation, and statistical analysis with uncertainty quantification.

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RevQSAR — Quantitative Structure–Activity Relationship Modeling

• Released RevQSAR for downstream analysis of SMILES + property matrices generated across the platform.
• Added multiple featurization methods: Morgan Fingerprints (ECFP), MACCS Keys, GraphConv embeddings, and ChemBERTa embeddings.
• Added clustering modalities: K-means, hierarchical, spectral, and Tanimoto-based clustering, with UMAP, t-SNE, and PCA projections for chemical-space visualization.
• Enables substructure and scaffold discovery to guide generative chemistry and lead expansion.

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Documentation

• Published full RevFEP and RevQSAR documentation pages with workflow guides and example pipelines.

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Expanded Analysis & Virtual Biology

• Introduced RevTS for transition-state analysis.
• Brought the full RevSim Virtual Cell experience online (interface and analysis).
• Delivered the full RevSingleCell analysis experience.
• Added RevScreen Protein-Ligand Docking.
• Released the full RevQS quantum-structure experience and full RevMut-PMX mutation free-energy analysis.
• Added Data Export capabilities across modules.
• Expanded SDF V2000 file support in the molecule viewer, and added an element-change mapping option for RevFEP.
• Improved docking algorithms and default settings.
• Retired the older RevGEx and RevCluster experiments to streamline the platform.

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Free Energy & Modeling

• Shipped RevFEP V2, a major upgrade to free-energy analysis.
• Added RevMD-Bind Residence Time, a new residence-time MD analysis.
• Released RevQSAR AutoQSAR modeling, with new MD Descriptor Analysis for descriptor-level insights within RevQSAR / RevAnalytics.

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Virtual Biology & Structure

• Introduced RevQS quantum-structure analysis (backend and interface).
• Added RevGRN for gene-regulatory-network analysis.
• Brought RevSim Virtual Cell online with initial virtual-cell analysis capability.
• Expanded RevSingleCell with new single-cell analysis features.
• Released new demo pipelines across these capabilities.

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Interface

• Launched Dark Mode V2, a refreshed dark theme with updated styling and smoother animations.
• Enhanced the molecule viewer with integrated file downloads and the ability to download key analysis data.
• Added on-screen guidance when selecting the CHARMM36 force field for MMPBSA.

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Docking

• Set the default RevDock docking box size to 30 for better out-of-the-box results.

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Improvements & Changes

• Added a friendly reminder when trying to reuse a trial plan.
• Continued RevFEP analysis enhancements.

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RevFEP — Free-Energy Perturbation Launch

• Launched RevFEP, powered by OpenFE, with input presets for quick setup.
• Introduced RevBench for benchmarking across the platform.

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Project Hub & Collaboration

• Launched Project Hub to organize pipelines into projects.
• Added Team Chat with Slack channel integration.
• Rolled out Real-Time Updates across the platform.
• Released new demo pipelines for RevFEP, RevMut-PMX, and RevQS.

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Molecular Dynamics & Docking

• Shipped RevMD-Bind MD Insights, a new MDInsights analysis for protein-ligand simulations.
• Added RevMut-PMX mutation free-energy enhancements.
• Enhanced RevDynamics post-processing and improved ligand detection.
• Added support for multi-model protein structures.
• Added on-screen guidance in Rigid Receptor and flexible docking.

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Platform

• Made Central Hub noticeably faster.
• Added credit-system support for RevConformer and RevADMET.
• Updated feature display categories for easier navigation.
• Delivered general Central Hub improvements.

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Documentation & Guided Workflows

• Set up Revilico Documentation and Solutions workflows (https://docs.revilico.bio/docs).
• Updated documentation implementations and integrated guided workflows into the right-hand side panel.
• Added demo pipelines across all features to preview generated data for each run.
• Added guided workflows in the right-hand side panel to assist users in conducting computational analyses.
• Fixed pipeline sharing issues to ensure all users can access generated data.

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Revilico Interpreter & Guide Revamp

• Revamped Revilico Interpreter and Guide for faster screen interpretation and seamless linking to the full documentation knowledge base.
• Added new models (GPT-5.2, Claude Sonnet 4.6) for smarter and more accurate interpretation.
• Improved Revilico Guide with integrated knowledge base querying and a transparent UI/UX.
• Integrated dual functionality of the Revilico Guide and Interpreter into a unified transparent UI with accessibility from the right-hand side panel.

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Docking & Virtual Screening

• Added Blind Docking and expanded box configuration in the Virtual Screening engine (Flexible Docking).
• Flexible Docking now supports multiplexed screens, enabling multi-receptor inputs against larger chemical libraries with CNN rescoring and pose refinements.

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Molecular Dynamics (MD)

• Improved MD simulation PDB extraction to create ensemble docking pipelines across multiple trajectories.
• Fixed issues related to erroneous structures generated during trajectory extraction.
• Enabled sub-pipeline termination across all MD features for multi-complex inputs, allowing users to stop full experiments across all sub-pipelines.

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Models & Large-Scale Pipelines

• Enabled large input set processing in Geometric Minimization and Thermochemistry workflows for scalable data abstractions.
• Stabilized ADMET, Pharmacophore Analysis, and Retrosynthesis capabilities for improved reliability and performance.

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Molecular Dynamics (MD)

• Upgraded MD engine to Revilico’s latest R&D version across all MD features.
• Added support for 4-point water models: TIP4P, OPC, and OPC3 for improved simulation accuracy.
• Expanded Ligand Membrane MD simulations with additional lipids and membrane systems for permeability analysis.
• Delivered performance optimizations resulting in faster MD simulation execution.

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Simulation Configuration

• Added UI components to configure solvents and solvent concentrations across MD workflows.
• Included ion concentration configuration to better resemble biological conditions.

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Analysis & Visualization

• Introduced RMSF plots and RMSF trajectory visualization tools with spatial fluctuation color mapping across protein surfaces.
• Enhanced Protein–Ligand MD analysis with detailed comparison tables including MM(PB/GB)SA, decomposition, and PCA insights for improved free energy estimation across trajectories.

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Models & Pipelines

• Updated Geometry Minimization and Thermochemistry Neural Network Potential (NNP) model weights.
• Added solvent configuration support to resemble physiological conditions.
• Synchronized Boltz Co-Folding and Virtual Screening Docking pipelines with Protein–Ligand MD input sequences.
• Standardized download file naming for improved analysis and seamless workflows.

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Retrosynthesis

• Upgraded Retrosynthesis Engine to the latest Revilico R&D version with architectural and performance improvements.

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Reliability & Operations

• Implemented automated Jira ticket creation on pipeline failures for improved incident tracking and operational visibility.
• New issues are automatically logged and triaged, enabling faster resolution within 24 hours.

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Docking & Pose Prediction

• Replaced classical empirical docking model with physics-based search algorithms powered by deep learning CNNs for more accurate poses and binding affinity calculations in Flexible and Ensemble Docking.
• Added the ability to extract receptor structures directly from Protein-in-Water MD simulations within defined timeframes and custom intervals for structural analysis across MD timescales.
• Introduced advanced configuration options to extract individual receptors at specific trajectory frame intervals for Ensemble Docking workflows.
• Enhanced Ensemble Docking workflows to allow grid box configuration across all trajectory structures.

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Visualization & UI

• Improved docking visualization UI to better identify and analyze binding sites and filter docking data effectively.

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Free Energy Calculations (Beta)

• Introduced ABFE and RBFE engines (Beta) enabling advanced alchemical transformations to compute ΔG binding of complexes.

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Platform & Architecture

• Implemented multiple stability enhancements across the platform.
• Implemented the Pharmacophore engine using Pritam Kumar Panda’s designs.
• Designed a new transcriptomic architecture for large-scale batch processing, improving scalability, reliability, and pipeline modularity for heavy workloads.

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Ligand Modeling

• Implemented ligand conformer search to generate low-energy 3D conformations, improving docking pose coverage and allowing chemists to evaluate energetic penalties across ligand–protein complexes.