SeeSAR

SeeSAR is an interactive, visual molecular modeling and drug design platform developed by BioSolveIT, designed to support medicinal chemists, computational chemists, and drug discovery teams at every stage of the design process. Built around the principles of speed, visual clarity, and ease of use, SeeSAR enables users to dock, design, and analyze compounds rapidly without a steep learning curve — making it equally accessible to seasoned drug design veterans and modeling beginners alike.

The platform integrates a comprehensive suite of scientifically validated tools — cited in over a thousand publications — covering structure-based and ligand-based drug discovery, fragment-based design, ADME property assessment, covalent docking, and ultra-large Chemical Space screening. Helpful features such as intuitive color coding, unoccupied binding pocket visualization, and on-the-fly molecule editing support informed, interactive decision-making throughout the entire compound evolution and prioritization workflow.

Core Modes and Workflow Capabilities

• Protein Mode: Drag and drop a protein structure or search an online database; the target is prepared within seconds for immediate use.
• Protein Editor Mode: Modify protein structures by exploring rotamers, introducing mutations, and customizing side chains.
• Binding Site Mode: Automatically detects the binding site of a ligand; allows precise expansion by adding individual residues or identifying empty pockets with a single click.
• Molecule Editor Mode: Edit molecules in 2D or 3D on-the-fly; edited molecules are immediately prepared for downstream tasks.
• Analyzer Mode: Estimate binding affinities using the HYDE scoring function, filter compounds by relevant parameters, calculate ADME properties, and gain full control over ligand–target interactions.
• Inspirator Mode: Discover new scaffolds, grow into free binding site cavities, and link molecules using fragment libraries for creative design solutions.
• Docking Mode: Dock compounds with a single click, screen compound libraries for actives, and evaluate results intuitively.
• Space Docking Mode: Perform structure-based virtual screening of ultra-large Chemical Spaces using the proprietary Chemical Space Docking® workflow.
• Similarity Scanner: Align compounds based on molecular similarity without requiring a target structure.

Chemical Space Docking® — Screening at Unprecedented Scale

• Synthon-based virtual screening approach enabling efficient screening of trillion-sized Chemical Spaces.
• Identifies novel, unlisted chemical entities and synthetically accessible compounds beyond on-the-shelf catalogs.
• Accumulates high-ranking compounds with superior predicted affinities.
• Supports an intervention-point workflow for controlled screening and chemical evolution from diverse starting fragments.
• Uses co-crystallized ligands or docking poses as templates and guides extension with growth vector constraints.
• Completes large-scale screening on standard hardware, reducing reliance on server farms or massive cloud resources.
• Integrates fragment-based drug discovery into ultra-large-scale screening.
• Visualizes atomic interaction feedback with HYDE and prioritizes results by ligand efficiency, lipophilic efficiency, and molecular properties.
• Leverages HPSee infrastructure for scalable external docking workflows while keeping data local and secure.

Target Handling and Protein Preparation

• Supports work on proteins, DNA, and RNA structures.
• Aligns and compares binding sites; detects and characterizes druggable pockets.
• Directly downloads PDB IDs and searches for structures containing a compound of interest.
• Refines target structures with integrated energy minimization and optimizes local protein–ligand geometries.
• Introduces specific protein mutations and explores alternative side-chain rotamers.
• Highlights conformational differences across aligned proteins and spots flexible side chains relevant for binding site evaluation.
• Defines conserved water molecules for docking and accounts for key waters as part of the binding environment.

Covalent Docking

• Docks covalent ligands with automated warhead handling covering 36 of the most common covalent patterns.
• Automatically transforms common covalent warheads into their bound states.
• Targets covalent residues including Cys, Ser, Thr, Lys, Tyr, Asn, and Gln.
• Samples covalent stereoisomers automatically and explores alternative stereochemistry near attachment points.

Fragment-Based Drug Discovery

• Expands and grows ligands using FastGrow for pocket exploration.
• Fuses, links, and merges fragments using ReCore for rescaffolding.
• Geometrically links fragments based on bound poses and combines overlapping hit motifs into improved designs.
• Supports fragment evolution with structure-based design feedback.
• Enables mix-and-match ideation for rapid scaffold diversification.

Ligand-Based Drug Discovery

• Performs 3D virtual screening to mine for novel chemotypes.
• Aligns compounds in 3D using FlexS for hypothesis generation and SAR analysis.
• Finds and aligns compounds by 3D similarity and builds aligned sets for downstream SAR analysis.
• Compares active and inactive molecules in a common reference frame.
• Uses aligned molecule sets from Similarity Scanner, docking, or binding site superpositioning.

Ideation and Compound Optimization Tools

• Discovers novel scaffolds and bioisosteres and optimizes compounds in real time.
• Finds and explores molecule decorations to satisfy unoccupied binding sites.
• Screens ultra-large synthetically accessible Chemical Spaces in 3D.
• Identifies novel hits beyond standard screening libraries and expands hits with make-on-demand follow-up ideas.
• Amalgamates overlapping moieties from different binders and links fragments based on 3D attachment geometry.
• Performs heteroatom walks to suggest improved analogs.

Core Computational Chemistry Capabilities

• Standard, template-based, and covalent docking powered by FlexX.
• Pose scoring with HYDE, including assessment of binding poses by molecular torsions and clashes.
• Ultrafast prediction of tautomers and protonation states.
• Management and filtering of molecule sets and compound libraries.
• Pharmacophore constraint support to guide computations.
• Measurement and labeling of distances, torsions, residues, and angles.
• Prediction of ADME and physicochemical properties.
• Prioritization of compounds for synthesis and experimental testing.

Upcoming: SAR and Activity Interpretation (SeeSAR 15)

• Derives 3D features from aligned molecules to identify key molecular features driving biological activity.
• Summarizes SAR across a compound series and turns SAR insights into pharmacophore constraints.

Six Key Reasons to Use SeeSAR

1. Efficiency meets enjoyment: Swift calculations and stimulating inputs help users find solutions in an inspiring way.
2. Designed for everybody: Radical simplicity delivers a satisfying experience for both drug design veterans and modeling beginners.
3. Full control: Informative color coding and comprehensive icons enable at-a-glance result evaluation and informed decision-making.
4. Easy to set up: Runs on