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

Capabilities in Flare V10 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