Cresset-BMD Flare v9.0.0
Cresset-BMD Flare is a comprehensive drug design platform including both structure-based and ligand-based methods.

Capabilities in Flare V9 include:
• Smart import and handling of protein-ligand complexes
• Accurate and reliable protein preparation
• Ligand preparation, including enumeration of stereo centers, stripping of salts, protonation at pH 7 and tautomer enumeration
• Sequence alignment and superimposition
• Accurate docking using Lead Finder
• Advanced ligand-based conformation hunt and alignment
• Pharmacophore building with FieldTemplater
• Electrostatic Complementarity maps and score
• Protein interaction potentials
• Qualitative Structure-Activity Relationship analysis using Activity Atlas and Activity Miner
• Quantitative SAR models of regression and classification using Field QSAR and machine learning methods
• Enumeration to generate libraries and arrays based on more than 100 popular synthetic chemistry reactions
• Chemical exploration of a hit or lead compound using Hit Expander
• R-Group Decomposition and Analysis
• Scaffold hopping and bioisostere replacement using Spark
• Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculations of ligand-protein binding free energy on individual protein conformations or on conformations ensembles from Molecular Dynamics
• Quantum Mechanics calculations on ligands
• Free Energy Perturbation simulations
• Support for the Open Force Field
• Molecular Dynamics
• Automatic creation of custom torsional parameters for ligands in support of Dynamics and FEP calculations
• 3D-RISM water analysis
• MD-based analysis of water thermodynamics with GIST
• Pocket detection to identify potential drug binding sites in the protein targets of interest
• Homology modeling to create reliable 3D structures for the targets of interest
• WaterSwap analysis for ligand and binding site energetics
• Minimization of protein ligand complexes using XED and OpenMM
• The Flare Python API