Changelog

​

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.

​

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.

​

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.

​

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.

​

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.

​

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.

​

Simulation Configuration

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

​

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.

​

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.

​

Retrosynthesis

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

​

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.

​

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.

​

Visualization & UI

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

​

Free Energy Calculations (Beta)

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

​

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.

​

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.