Biologics Suite

Comprehensive Protein Modeling

• Complete set of homology modeling tools, including both rapid and advanced methods
• Chimeric and multimeric models
• Advanced sequence tools for multiple alignment, with extensive annotation options
• Protein structure quality analysis
• Identification of consensus elements in structural families/homologs

 Advanced Features for Protein Engineering

• Protein aggregation prediction
• Identification of hot spots for proteolysis, glycosylation, deamidation, and oxidation
• Residue-based analysis of energies, solvent-accessible surface areas, and hydropathy
• Cysteine scanning to identify residue mutations for potential cysteine-cysteine disulfide bonds
• Automated residue scanning to predict relative stabilities as well as changes in solvent‑accessible surface area, pKa, and hydropathy

Antibody Modeling

• Automated intuitive workflow
• Prediction of CDR from sequence
• Rapid prediction using curated antibody database
• Advanced ab initio loop prediction using Prime
• Database management tools for simple incorporation of new/proprietary structures, and allows use of multiple databases in modeling

State-of-the-Art Protein-Protein Docking

• Well-validated docking code, PIPER; for more information please visit the PIPER website.
• Special antibody and multimer modes

Advanced Simulations

• Access to Schrödinger simulation tools
• Advanced molecular dynamics (MD)
• Extensive Free Energy Perturbation (FEP) tools
• Large-scale, low mode (normal) search for domain movement
• Quantum mechanics/molecular mechanics (QM/MM) predictions of binding site reactivity

Small-Molecule Drug Discovery Suite

Wide Range of Virtual Screening Options, Spanning the Spectrum of Speed vs. Accuracy Tradeoffs

• 2D/3D QSAR with a large selection of fingerprint options
• Shape-based screening, with or without atom properties
• Ligand-based pharmacophore modeling
• e-Pharmacophore modeling incorporating ligand-receptor interaction energies
• Flexible ligand docking with industry-leading Glide
• SIFt — structure interaction fingerprint analysis
• Induced-fit docking with receptor flexibility
• Covalent docking
• 2D ligand interaction diagrams

Advanced Computations to Estimate Binding Affinity and to Rank-Order Compound

• Embrace post-docking refinement
• Prime MM/GBSA
• Free energy perturbation (FEP) theory
• Linear interaction approximation (LIA)
• QM-polarized ligand docking

Analyses to Predict, Prepare, Refine and Characterize Target Structureand Binding Modes

• Protein crystal structure refinement
• Protein structure analysis and homology modeling
• GPCR and hERG modeling
• Protein binding site identification and analysis
• Multiple binding mode prediction

Complete Set of Utilities to Prepare, Analyze and Filter Ligand Structures and to Create and Design Ligand Libraries

• 2D to 3D structure conversion, with emphasis on bioactive conformers
• Tautomeric state enumeration and analysis
• Ligand interaction diagram
• Commercially-available compound database
• Flexible ligand superposition
• Combinatorial library creation
• Core hopping
• Filter compound libraries based on predicted ADME properties
• R-group analysis

General Modeling Tools That Can be Applied Across a Wide Range of Chemical Systems

• High-performance QM calculations, in gas phase and in solution
• MM/MD simulations, with implicit or explicit solvents
• Small molecule and macromolecular conformational analyses
• Mixed-mode QM/MM calculations for ground state and reactivity studies

Fully Supported by State-of-the-Art Visualization and Workflow Automation Tools

•  Unified graphical user interface, Maestro, that serves all computations
• Publication-quality graphics and flexible analysis
• KNIME Extensions and customizable workflows
• Python API