Schrodinger Suite 2024-1 Advanced Edition

Small Molecule Drug Discovery

Platform Environment
Maestro Graphical Interface
- Improved usability for several Project Table dialogs including Change Property, Substructure Count, Add Property, Add Sequential Index Property, Add Standard Molecular Property, Redo Calculation, and Total Surface Area
- Improved usability of the Find Toolbar by adding a close button and “Search in Progress” indication
Workflows & Pipelining [KNIME Extensions]
- Stabilized version of the KNIME generic LiveDesign protocols
- New node for pKa prediction using Epik 7
- Added support for AB-FEP files to FEP+ reader node
Target Validation & Structure Enablement
Protein Preparation
- Improved accuracy of ligand ionization/tautomeric state predictions in the Protein Preparation Workflow using ML-enabled Epik by default
- Ability to optionally provide sequence information via FASTA file when filling in missing loops
Multiple Sequence Viewer/Editor
- Ability to export sequences and annotations to seqD file
Binding Site & Structure Analysis
Desmond Molecular Dynamics
- Added Radial Distribution Function (RDF) analyzer in Trajectory Plots

Hit Identification & Virtual Screening

Ligand Preparation
Empirical and QM-based pKa Prediction
- Improved accuracy in empirical corrections for Macro-pKa from a new ML-based algorithm used by default
Lead Optimization
FEP+
- Improved functionality of FEP+ Panel-managed trajectories can now be moved out of the FEP+ entry group, to retain it in the project table
Protein FEP
- Mutation generation will now ignore water molecules for sidechain placement
Solubility FEP
- Ability to compute hydration free energies from Solubility FEP with useful blood brain barrier penetration correlation: Hydration-only mode is now available from Advanced Options of the Solubility FEP panel
Quantum Mechanics
- Employ different basis sets by atom in Jaguar Transition Search
- Predict and view NMR spectra based on DFT chemical shifts and spin-spin couplings
- Added support for analytic basis sets with high angular momenta including cc-pvXz and def2 basis sets up to QZ
- Added support for composite 3c-functionals: HF-3c, PBEh-3c, HSE-3c, B97-3c, r2SCAN-3c, and wB97X-3c

Biologics Drug Discovery

- Improved accuracy in antibody modeling with new curated antibody database that now excludes redundant and/or poor-quality PDB structures
- Option to export all 1000 unclustered raw poses from PIPER protein docking
- Report the % humanness of the Heavy and Light chain on the grafted model in Antibody humanization by CDR grafting
- Export aggregation profile images in png format
- Report detailed patch characteristics in Protein Patch calculations
- Easily perform detailed analysis of residue scanning results with new csv file containing mutant descriptions and energies

Materials Science

GUI for Quantum ESPRESSO
Product: Quantum ESPRESSO (QE) Interface
- Convergence monitor for the nudged elastic band (NEB) calculations
- Workflow for computing dielectric constant (command line)
- Support for parallel computation of Phonon calculations (command line)
- Option to display discrete frequencies from dynamical matrix for phonon DOS
- Support for phonon calculations with Hubbard U potentials for LDA+U
- Support for mean square displacement analysis over an existing AIMD trajectory
Materials Informatics
Product: MS Informatics
- DeepAutoQSAR: Access from the Task menu under Materials Informatics
- Formulation ML: Machine-learning-based property predictions using chemical formulations
- Machine Learning Property: Improved machine learning models
- MD Descriptors: Bond, angle, torsion, and vdW energies computed as descriptors
- MD Descriptors: Improved efficiency with the MD simulation protocol
Coarse-Grained (CG) Molecular Dynamics
Product: MS CG
- CG FF Builder: Implicit charge assessment by dielectric constant
- Automated DPD Mapping: Support for multiple ionization states (command line)
- Automated DPD Mapping: Support for pre-defined patterns for use in mapping (command line)
- Support for including CGFF file (*.json) information into other CGFF files
Reactivity
Product: MS Reactivity
- Schrödinger Nanoreactor: Chemical reaction discovery and analysis module based on AIMD and semiempirical QM (xTB) methods
- Auto Reaction Workflow: Improved speed in calculating custom rates and Keq
Microkinetics
Product: MS Microkinetics
- Workflow module for microkinetic modeling of chemical reaction rates
MS Maestro Builders and Tools
- Complex Enumeration: Support for the use of two ligand libraries as input
- Complex Enumeration: Option to specify the number of unique ligands
- Move Selected Atoms: Workspace tool to rotate/translate selected atoms
Classical Mechanics
- Polymer Crosslink: Option to block formation of specific chemical structures
- Molecular Deposition: UI update with improved control of adsorbate setup and simulation protocols
Quantum Mechanics
- TST Rate: Jobs launched to queue
Education Content
- New Tutorial: Microkinetic Modeling
- New Tutorial: Machine Learning for Formulations
- New Tutorial: Nanoreactor
- New Tutorial: Modeling Receptor Binding in an Olfactory Protein
- New Tutorial: Building a Coarse-Grained Skin Model using Martini Force Field
- Updated Tutorial: Activation Energies for Reactivity in Solids and on Surfaces
- Updated Tutorial: Molecular Deposition