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Announcements

[Update]Add several small molecule drug design modules​

Release Date: Aug 31, 2023

This update is version 1.1.1, including：

  • Add new small molecule drug design modules:
    • Similar Molecules Search: Generate molecular fingerprints of query molecules based on various methods, and match their similarity with target molecules.
    • Substructure Search: Match target molecules' identical parts based on substructure SMARTS.
    • Compound Clustering: Aggregate molecules with similar properties into one category according to the number of classifications.
    • Maximum Common Substructure: Find the maximum common substructure in target molecules.
    • Binding Stability: Perform 3ns full-atom simulations on complex to evaluate the stability of the binding site.
  • Add Loop Optimization module: Provides the function to optimize the conformation of protein flexible loop structures.
  • Merge: Can merge protein files and small molecule files.
  • Export: Can export protein and small molecule files within Hermite.
  • Optimize 2D experience and improve the convenience of drawing repetitive objects.
  • Optimize 3D result visual and enhance the 3D Workspace stereoscopic sense and recognition of 3D-interaction.

[Release] Hermite 1.1.0 Launched​

Release Date: May 27, 2023

This update is version 1.1.0, including：

  • Add new large molecule drug design related modules
    • Protein-Protein Docking: A protein-protein rigid docking tool based on the Fast Fourier Transform (FFT) algorithm.
    • Sequence Alignment: A protein sequence alignment tool based on the Multiple Sequence Alignment (MSA) algorithm.
    • Antibody Numbering: A tool for annotating the CDR region of antibody sequences based on antibody numbering systems (supported: IMGT, Kabat, Chothia).
    • Antibody Humanization: A tool for humanizing antibodies based on databases and statistical models. Supports CDR region labeling and transplantation, human source antibodies, and provides graphical functions for antibody humanization.
    • Antibody Properties: A tool for evaluating the developability of antibodies (including: viscosity, aggregation, clearance rate, isoelectric point, extinction coefficient, etc.) based on databases and statistical models. Also supports the structural modeling of the variable region (Fv) of antibodies.
    • Nanobody Properties: A tool for evaluating the developability of nanobodies (including: aggregation, clearance rate, isoelectric point, etc.) based on databases and statistical models.
    • PTM Prediction: A tool for predicting protein post-translational modification (PTM) sites (such as phosphorylation, glycosylation, ubiquitination, nitrosylation, methylation, acetylation, etc.) based on artificial intelligence algorithms.
    • AI Protein Mutation: A tool for quickly predicting the difference in thermal stability before and after protein mutation based on artificial intelligence algorithms, integrating multi-modal features such as protein structure and dynamic information.
    • Protein Alignment: A tool for 3D superimposition of protein structures (based on backbone, Ca, sidechain) and supports the superimposition of multiple protein structures.
  • Add FEP Protein Mutation module: In the FEP calculation process, support the amino acid in the protein to undergo Alchemical Transform changes, and accurately calculate the impact of point mutations on protein properties (currently only the function of predicting the difference in thermal stability before and after mutation is open).
  • Add Uni-QSAR module: A quantitative structure-activity relationship (QSAR) modeling and prediction tool based on the combination of various artificial intelligence (deep learning, machine learning) models, and on the basis of 1D and 2D molecular descriptors, a new 3D molecular descriptor based on the pre-trained model of molecular 3D structure (Uni-Mol) is added, greatly improving the accuracy of QSAR models.
  • Add VD-Gen module: A molecular de novo design function based on the Virtual Dynamics (VD) artificial intelligence algorithm, dependent on the protein pocket.
  • Add small molecule 3D structure editing capabilities: Support for 3D editing of small molecule structures stored in .sdf/.mol files. Including: adding/modifying atoms, adding and subtracting bonds, adjusting bond levels and dihedral angles, hydrogenation of small molecules, and energy minimization of small molecules.