MOE 2022.02

2022.02

The 2022.02 release of Chemical Computing Group's Molecular Operating Environment (MOE) software includes a variety of new features, enhancements and changes that are summarized in this document.

Core System

Updated Version of Flexera License Manager. MOE now uses an updated version of the Flexera license manager. The license manager server components lmgrd, chemcompd, and lmutil have all been updated to version 11.18.1. This version is compatible with Apple Silicon M1.

To run MOE 2022.02, license manager servers must be updated to version 11.18.1 or greater and restarted.

Note that older versions of MOE will continue to run with the updated license manager.

Minimum Java version. MOE 2022 now requires Java 8 or higher.

Officially supported Java platforms. MOE 2022 officially supports both Oracle Java and OpenJDK.

Supported architectures. MOE 2022.02 is compatible with the following architectures:

Operating System MOE architecture code
NEW! Apple Silicon M1 armm
Linux (64-bit) lnx64
macOS (64-bit) mac64
Windows (64-bit) win64

Apple Silicon. FlexNet v11.18.1 and XQuartz 2.8.0 are required to run MOE on Apple Silicon M1. Please note that XQuartz 2.8.1 introduced a text rendering performance bug and should not be used.

macOS version. FlexNet v11.18.1 officially supports only macOS 10.14, therefore, macOS 10.14 is recommended when running the license server on macOS.

Windows 11. MOE 2022 is compatible with Windows 11.

GPU. GPU acceleration in MOE 2022.02 requires a CUDA-enabled GPU with an NVIDIA display driver. The minimum supported CUDA version is 10.0, with a minimum compute capability of 3.5. The required CUDA components are part of the NVIDIA display driver; the CUDA SDK is not required to run MOE's GPU code.

Official discontinuation of support. Support for the all 32-bit versions of MOE is officially discontinued; these versions are no longer available. Support for Internet Explorer 10 and 11 is also officially ended, i.e. Internet Explorer is no longer supported in MOE.

NEW! GPU Information. MOE | Help | GPU Info opens the new GPU Information panel that reports which GPU device (the default device) will be used for GPU calculations. The GPU driver and compute capability versions are displayed, along with memory, clock speed, number of multiprocessors, number of CUDA cores, and GPU UUID. The compatibility with MOE GPU-accelerated applications is also indicated.

Carbohydrate Builder

Carbohydrate detection and depiction. Support for carbohydrate detection and display has been added.

Database Viewer Display. The Database Viewer has new molecule display features and also supports the display of graphic objects.

Database Viewer Find. The DBV search capability has been enhanced as follows:

Database Viewer Plot. The Database Viewer plot is now an SVL panel, and has the following new features.

Database Viewer Print. The Database Viewer printing facility offers the following updates:

Database Viewer Molecule Name. Database molecule naming options have been added as follows:

Database Viewer Coloring. The Database Viewer Field Coloring panel has been enhanced as follows:

A new option controlling DBV text coloring has been added to the Configuration Options panel Database Viewer page. Invert text color on dark background, when enabled, inverts the text/foreground color when the cell has a dark background color. This may make the text more readable when field coloring renders the cell background dark.

Database Browser. The Database Browser has been updated as follows:

    • RC variables. The RC variable dbbrowse.tag.suffix and dbbrowse.tag.suffix.dbbrowse_Dock control the suffix used for the browsed structures tag.

Database Calculator. The option Use 0 for Empty Cells has been added to treat empty cells as 0 for row-wise operations.

Database Menus. Database Viewer menus for editing and selection have been updated as follows:

Menu Menu Item Description
DBV | Edit Select Fields New menu item to open the Select Fields prompter.
DBV | Field Popup Select Fields Updated. Multiple field names can now be specified in the same line; use single quotes to enclose field names that contain spaces. A new Apply button, or equivalently, Shift-Return, performs the search while leaving the prompt open.
DBV | Field Popup | Select Entries Numeric
Not Numeric
New options for character fields select entries containing or not containing text that represents numeric values.
DBV | Field Popup | Select Entries First Occurrence Renaming of the menu item "Unique".
DBV | Field Popup Clear Selected New option to delete the contents of the cells of the selected entries in the current field upon confirmation.
DBV | Field Popup Edit Selected New menu option to open the Edit prompter for the cells of the selected entries in the current field.
DBV | Molecule Field Popup Convert To Sequence New option added for 'moe' and 'molecule' fields, to convert molecule to sequence-only by deleting all atom information.
DBV | Edit New Entry When there are selected atoms in the system, Selection in the Add Entry panel will automatically be set to Selected Atoms (otherwise it will be set to Ignore).

Plots.

Graphic Object Export. Export of graphic objects via Print | Export Page has been enhanced with the following features:

File formats. Support for the following file formats has been added:

Electron Density in applications. DSN6 map and CIF structure factor support have been added to Energy Minimize and Dock.

2D Overlay. The MOE | Footer | 2D Overlay has been updated as follows:

Protonate3d. Support for U (uracil) has been added.

Torsion Profile. A new Calculate Charges option has been added.

Widgets. The following updates have been made to widgets that compose panels.

PSILO Query. The PSILO page of the MOE | File | Open panel has been updated to include Database as an identifier, compatible with the new PSILO federated database framework. The result of the query is a listing of the contents of the database.

Third party software. MOE 2022.02 supports:

MOE menus. The following changes have been made to MOE menus.

Name Menu Item Description
MOE | File | New Combinatorial Library (MOE/web) Launch the MOE web application Combinatorial Library Enumeration in a new tab of the default browser.
MOE | RHS | Constraints Restraints
Clear
Open the Restraints prompter.
Clear restraints associated with the currently selected atoms.
MOE | Compute | Conformations Dihedral Contour Plot Launch the updated Dihedral Contour Plot application. This menu item was previously located under MOE | Compute | Simulations.
MOE | Help GPU Info Open the new GPU information panel.

Applications

GPU Acceleration. Performance speedups through use of GPU have been realized for the following computations.

Ensemble Protein Properties. Options have been added to the Protein Properties Residue Table:

An alternative method for submitting large Protein Properties jobs to job management systems has been added which better optimizes data distribution.

DNA/RNA Builder. Support for mutating to/from arabinose RNA, which has a different chirality at C2', has been added.

Antibody Modeler. The Antibody Modeler has been updated as follows:

Sequence Annotation. IMGT constant domain numbering has been added.

PLIF Analyze Ligand Tiles

PLIF Analyze. DBV | Compute | PLIF | Analyze has been updated as follows:

MOE Projects. The following are updates related to MOE Project Databases:

Protein Design. The Protein Design application has been updated as follows:

Updated reaction files. Reaction files in MOE have been updated, and are now all in *.rxn format. Applications using reactions have been concomitantly updated:

HMR. Support for Hydrogen Mass Repartitioning, which redistributes mass from heavy atoms to light atoms to slow down motion without changing the overall mass of the system, has been added to:

The change allows for increasing the timestep from 2 fs to 4 fs, thus reducing simulation times by a factor of two.

Note: Care must be used when applying this technique; for example, in very small structures, such a mass redistribution can significantly alter the calculated properties of the system.

AMBER MD. When running an AMBER dynamics simulation, the AMBER command used for each stage is output during that stage into a .cmd file.

Descriptors. New descriptors are available from the Calculate Descriptors panel (DBV | Compute | Descriptors | Calculate):

Name Description
arorings Number of aromatic rings
a_nNO Number of nitrogen and oxygen atoms
RBC Number of rotatable bonds; this descriptor supersedes b_rotN, which is now obsolete
pro_cdr_len* Antibody CDR length
pro_Fv_chml* Fv charge separation (VH-VL difference)

*Thornsteinson, N., et al.; MABS 13(1) (2021) On-line. https://doi.org/10.1080/19420862.2021.1981805

The following descriptors have been updated:

Name Description
b_max1len Now calculated based on a chain of rotatable bonds rather than just formal single bonds.
mutagenic Now calculated based on detection of mutagenic chemical groups.
reactive Now calculated based on detection of reactive chemical groups.
rsynth SMILES strings updated.

Sketcher Reaction

Sketcher. The MOE Sketcher web application now supports reactions and enhanced query annotations.

Combinatorial Library Enumeration Web App

NEW! Combinatorial Library Enumeration. The Combinatorial Library Enumeration (CLE) web application is a reaction-based library enumerator. It uses a novel probabilities-based virtual compound enumeration algorithm that allows for browsing and tuning the fully-enumerated library interactively without the library actually having to be fully-enumerated. The application provides the following key features:

MOEsaic. MOEsaic, the web-based application for Structure Activity Relationship (SAR) and Matched Molecular Pair (MMP) analysis, offers a major new feature, MOEsaic Dock. Docking calculations can now be launched on-the-fly from MOEsaic and the results visualized in the MOEsaic interface. The calculations are performed in the background so that the MOEsaic interface remains available for interactive use.

MOEsaic has also been updated with the following enhancements:

Data Files

$MOE/lib files. The following changes have been made to $MOE/lib:

Name Description
$MOE/lib/abref/IgC.moe.gz New Ig constant domain profile for Ig constant domain identification and IMGT constant domain numbering.
$MOE/lib/carbo.mdb Updated to include all carbohydrates in the SNFG nomenclature.
$MOE/lib/NMR_ref.mdb Additional scaling factors have been added to the NMR reference database.
$MOE/lib/pdbx.xsd.gz Updated RCSB PDB XML specification.
$MOE/lib/reactions/clip
$MOE/lib/reactions/combi
$MOE/lib/reactions/covalent
$MOE/lib/reactions/medchem
The reaction files included in MOE have been updated as follows:
  • The .rxn format is now used for all reactions. .rdf files are still supported.
  • $MOE/lib/clipreactions has been replaced by the clip sub-folder.
  • The files in the combi folder replace those reaction files formerly housed in $MOE/lib/reactions.
  • The covalent reactions in $MOE/lib/reactions/covalent have been updated.
  • The files in the medchem sub-folder replace the database of reactions $MOE/lib/medchem_rxn.mdb. Note that use of reaction database is still supported.
$MOE/lib/Sigma.csv.gz About 18000 compounds from the Sigma-Aldrich database; replaces combi_reagents.mdb as the default reagent catalog for CLE and Combinatorial Library.

Sample files. The following changes have been made to $MOE/sample and $MOE/sample/mol, the directory of sample molecular data files. Please note that all .moe files in $MOE/sample/mol/ are now gzipped.

Name Location Description
3ln1_dock.mdb
3ln1_query.ph4
3ln1_rec.moe.gz
$MOE/sample/mol Examples of pre-docked data files for MOEsaic Dock.
bite.fst
bite.moe.gz
dart.fst
dart.moe.gz
Fv_vhh.fst
Fv_vhh.moe.gz
Ig_scfv2.fst
Ig_scfv2.moe.gz
$MOE/sample/mol Examples of query and custom template files for building custom antibody models; these files are used by $MOE/sample/ab_custom.svl.
FMN_riboswitch_example.moe.gz $MOE/sample/mol/DNA-RNA Example of an FMN riboswitch (RFN element)
quinazolinedione_scaffold.mol $MOE/sample/mol Example reagent file used in the Combinatorial Library Enumeration tutorial.
scfv_sequences.mdb $MOE/sample/mol scFv sequence data example.
ab_custom.svl $MOE/sample Sample SVL file providing examples of how to build custom antibodies using ab_Model.
chiview.svl $MOE/sample Sample SVL file for displaying chirality annotations.

SVL Programming

The following are SVL functions that have been added to or modified in MOE. Please consult the SVL Function Index for more information.

Function Description
ab_Annotate Creates or modifies sets, and optionally renumbers residues, colors atoms, residues, and ribbons, and re-orders and splits chains, based on domain information.
ab_ClassifyDomains Identifies antibody and TCR variable domains and antibody constant domains.
ab_Model Custom template configurations are now supported.
aRacemicBits
aSetRacemicBits
Reports/sets atom V3000 STERAC/STEREL bit information on atoms.
ctab_Cat Catenates a list of ctabs and returns the result.
ctab_Extract Updated to accept an MDB mol or a SMILES string.
ctab_aIsLight Returns a mask of light atoms.
cDFT
cDFTinv
rDFT
rDFTinv
Multithreaded Discrete Fourier Transform of complex and real data.
db_Calculator Now callable directly from the SVL command line.
dbv_DisplayAttributes Gets and sets Database Viewer display attributes.
gpu_* SVL programming interface for performing GPU CUDA calculations.
gr_decode_Grob Parses an image/grob string, creates the grob, and returns the grob key of the parsed image.
gr_fread_Grob Reads and parses an encoded grob from a file, creates the grob, and returns the grob key of the parsed image.
rcsb_download Updated to accept mmcif as an option which, when enabled, preferentially downloads CIF files from the RCSB.
wt_PlotBubbleHelp
wt_PlotSetBubbleHelp
Functions for implementing interactive plot operations. wt_PlotBubbleHelp is used as the value for Plot attribute bubbleHelpCmd, and takes as argument a callback function name or pointer which will be executed to create the mouse-position-dependent bubbleHelp.
PlotPickInfo Returns information about the tolerance of the mouse click region in the plot.
PlotCopyToClipboard Copies plot data values onto the clipboard.
sm_ExtractUnique Atom square bracket notation is less strict than the Daylight specification: when the hydrogen count satisfies normal valence requirements, the H count is not output. For example, a chiral carbon atom with 3 heavy neighbours would be emitted as [C@@] instead of [C@@H]. If hard-coded SMILES strings are being used for direct comparisons, they should be regenerated.

The following SVL functions are now deprecated:

Function Superseded by
dft
dftinv
rdft
rdftinv
cDFT
cDFTinv
rDFT
rDFTinv
exe_open_shell The use of this function is no longer supported. exe_open should be used instead.