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
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