Schrodinger Suite 2023-4 Linux

Schrödinger Software Release 2023-4 – Date: November 2, 2023

Hit Identification & Virtual Screening

Ligand Preparation

Empirical and QM-based pKa Prediction
– Improved Lewis structure canonicalization in Epik [2023-4]

Binding Site & Structure Analysis

Desmond Molecular Dynamics
– Radial Distribution Function (RDF) Panel can now ‘Group’ sites by monomers [2023-4]
Mixed Solvent MD (MxMD)
– Added support for fragment-size probes [2023-4]

Target Validation & Structure Enablement

AlphaFold Download / Process
– Added support for processing AlphaFold2 models and PAE files created through ColabFold [2023-4]
Multiple Sequence Viewer/Editor
– Full release of ‘Align by Family’ panel (removed beta label) [2023-4]
– Added T-Cell receptors as newest protein family recognized and property annotated with sequence features [2023-4]
– Support for family aware alignment of T-Cell Receptor sequences to enable downstream applications like homology modeling [2023-4]

Platform Environment

Maestro Graphical Interface
– Improved functionality and enhanced usability in the new embedded Workspace Sequence Viewer [2023-4]
– Improved Scatter Description capabilities: An updated charting tool provides a more intuitive interface, interactive features for data exploration, and extensive customization options for generating scatter Descriptions [2023-4]
– New Lasso Selection: Draw a freeform selection path with superior precision around specific atoms or regions compared to Marquee Selection [2023-4]
– New 3D Builder behavior preference to automatically minimize newly added fragments [2023-4]
– Redesigned ‘Find Toolbar’ boasts an improved user interface with new functionalities such as sequence search and enhanced "Search by SMARTS" with access to the Sketcher [2023-4]
– Added support for Nonstandard Amino Acids in the 3D Builder [2023-4]
– Improved user interface for several Project Table dialogs [2023-4]:
. Combine Properties
. Copy Property
. Delete Properties
. Clear Values
– Added menu option to move selected entries to the top or end of their current group [2023-4]
– Enhanced surface visuals through texture mapping, utilizing per-vertex texture coordinates to enrich detail and color vibrancy [2023-4]
– mmCIF files (.cif) are now treated the same way as PDB files (.pdb) upon import into Maestro, with atoms automatically colored by element for improved visualization [2023-4]
Force Field
– FFBuilder now uses the QRNN-TB neural network potential as its default reference method. Typical FFBuilder jobs run 3-5X faster [2023-4]
Workflows & Pipelining [KNIME Extensions]
– LiveDesign connection node supports Single Sign-On and reconnection to hosts running different LiveDesign versions [2023-4]
. (KNIME-6251)
. (KNIME-6253)
– LiveDesign connection node can be connected to the Upload as LiveDesign node [2023-4]
. (KNIME-6255)
– LiveDesign settings are stored for several hosts as profiles in KNIME preferences panel [2023-4]
. (KNIME-6238, KNIME-5774)

Lead Optimization

Ligand alignment
– Improved performance of macrocycle alignment for cis- and trans-bond containing macrocycles [2023-4]
FEP+
– Improved analysis of multiple physical properties in FEP+ panel [2023-4]
. Small Molecule FEP: Relative Solvation, Relative Binding
. Solubility FEP: Hydration, Dissolution
. Protein FEP: Selectivity, Thermostability
– Additional settings in Advanced Options Panel [2023-4]
. Equilibration time
. Simulation time is split into solvent/complex/vacuum
– Improved accessibility for submitting jobs to web services [2023-4]
Constant pH Simulations
– Trajectory Player: Improvements to the Lambda Dynamics [2023-4]
FEP Protocol Builder
– Ability to run FEP Protocol Builder on user defined submaps [2023-4]
Macrocycles
– Introduced the -parameter command line argument for macrocyclize.py to individually specify parameters [2023-4]
. The -parameter argument expects a=argument, whereis one of several runtime parameters that can be inspected through the -write_param_file option.

Schrödinger Softwareprovide accurate, reliable, and high performance computational technology to solve real-world problems in life science research. It can be used to build, edit, run and analyse molecules. The Schrödinger-Suite of applications have a graphical user interface called Maestro. Using the Maestro you can prepare your structure for refinement. The following products are available: CombiClide, ConfGen, Core Hopping, Desmond, Epik, Glide, Glide, Impact, Jaguar ( high-performance ab initio package), Liaison, LigPrep, MacroModel, MCPRO+, Phase, Prime, PrimeX, QikProp, QSite, Semi-Empirical, SiteMap, and Strike.

Release 2023-4 – New Features

Schrödinger, LLCprovides scientific software solutions and services for life sciences and materials research, as well as academic, government, and non-profit institutions around the world. It offers small-molecule drug discovery, biologics, materials science, and discovery informatics solutions; and PyMOL, a 3D molecular visualization solution. The company was founded in 1990 and is based in Portland, Oregon with operations in the United States, Europe, Japan, and India.