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.
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|
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. 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 detection and depiction. Support for carbohydrate detection and display has been added.
- Symbol Nomenclature for Glycans (SNFG) representation. Detected carbohydrates can be depicted using SNFG symbols.
- Updated carbo.mdb. $MOE/lib/carbo.mdb has been updated to cover all carbohydrates in the SNFG nomenclature.
- Carbohydrate Builder. The Carbohydrate Builder
has been updated as follows:
- SNFG symbol display has been added.
- The Carbohydrate Builder is now attachable/detachable.
Database Viewer Display. The Database Viewer has new molecule display features and also supports the display of graphic objects.
- menu panel. The menu has been replaced by a panel in which the molecule, hydrogen, and label display modes can be set.
- Carbohydrate molecule display. A carbohydrate display mode has been added in which carbohydrates are automatically detected and displayed using SNFG symbols.
- Sequence-only molecule display. A sequence-only display mode has been added in which proteins and nucleic acids are displayed as sequence data in FASTA format.
- Polar hydrogen display. Option to display just polar hydrogens.
- Chirality display. Option to display atom stereochemistry with bond wedges and chirality labels; only applicable when displaying molecule in 2D.
- Molecule Name. The display of the molecule name is now enabled by default.
- Per-field unified view. Unified view mode is now enabled from the menu and applies only to the current field; the option is only available in 3D display mode.
- Display of images and graphic objects. Character fields containing PNG image or MOE graphic object (grob) data encoded as strings will automatically display the grob/png image.
- Zoom and translate. 2D, carbohydrate, grob, and PNG images can be zoomed with Ctrl+Middle-drag and translated with Middle-drag.
Database Viewer Find. The DBV search capability has been enhanced as follows:
- Multiple search criteria in a single query. Multiple numeric and text searches (e.g. >10 <30) can now be specified in the same query line; this is useful when searching All Fields, Number Fields, or Text Fields.
- And and Or modes for combining search criteria. When multiple criteria are present in a single search line, And requires that all criteria be satisfied for a successful match, while Or requires just one to be satisfied.
- Searching numerical vectors. For database cells containing a vector of numerical values, only one of the values in the cell is required to match, in either And or Or modes, for a successful search.
- Wildcard text search now optional. The use of wildcards in
text field searches is now optional. The match options have
been updated to:
- Partial. When enabled, exact substring match is performed.
- Wildcards. When enabled, search text is interpreted using findmatch syntax to perform the search. When disabled, special characters (e.g. * or [ ) will not be treated as wildcards.
- Case. When enabled, the search is case-sensitive.
Database Viewer Plot. The Database Viewer plot is now an SVL panel, and has the following new features.
- Specify plot type. The type of plot – Data Plot (corresponds to former default plot type), Correlation Plot, Field Histogram – is now specified at the time that the plot is opened using .
- Attach/Detach capability. The DBV plot can now be detached and reattached.
- Multiple plots. Since DBV plots can be detached, multiple plots are now supported.
- Zoom and translate. The scroll wheel can be used to zoom the plot display, and Middle-drag can be used to shift the display in X and Y.
- Deselect. Ctrl-click will deselect a plot point. Shift-drag sweeps out a selection rectangle that is ANDed to the current selection; i.e. the resulting selection will be points that were already selected and that fall in the Shift-selection region.
- Plot Selected Fields. New option in resets the plot to display the data in the currently selected fields in the Database Viewer.
- Logarithmic scale. In the panel, Scale | Logarithmic is a new option to turn on log scaling on a data axis; i.e. the Y-axis in Data Plot, and X- and Y-axes in Correlation Plot.
- Ligand depiction in bubbleHelp. The bubbleHelp on plot points now displays a ligand depiction in addition to the values of the fields appearing in the plot.
- Double-click to scroll to entry. Double-clicking on a plot point will scroll the entry display to bring the corresponding entry into view.
Database Viewer Print. The Database Viewer printing facility offers the following updates:
- Support for mixed PNG, graphic object, carbohydrate, 2D and 3D display. Double-clicking in a cell containing an image or a graphic object opens the Export Image panel.
- Scrollbars added to print preview.
- Mol Style. New option to display carbohydrates using (SNFG) representations; non-carbohydrates will be displayed in 2D mode.
- Use Existing 2D Coordinates. New option; enable only if database cells contain precalculated 2D coordinates.
- Display Chirality. New option to display atom stereochemistry with bond wedges and chirality labels when enabled; only applicable when displaying molecule in 2D.
- Display All Hydrogens. New option to display all hydrogens on displayed atoms.
- Do Not Color Hetero Atoms. Recasting of the previous "Color Het Atoms". The option is disabled by default.
Database Viewer Molecule Name. Database molecule naming options have been added as follows:
- Automatic naming options. The database molecule name can now be automatically set to either the Chain Name, Chain Tag, or Auto (use first non-empty chain tag, otherwise chain name).
- The option to set the database molecule name on molecule creation in the database has been added to the New Database, Add Entry, and Copy Molecule from MOE panels.
- Molecule Name. The
panel has been updated as follows:
- Extract From Molecule has a new Chain Tag option.
- Store In Molecule has been updated with new Tag and Name options, a text field for specifying a name suffix for the Concatenate to existing name option, and a new Use Field Precision option for using the currently displayed numerical precision when setting the molecule name from a numerical field.
Database Viewer Coloring. The Database Viewer Field Coloring panel has been enhanced as follows:
- Streamlined layout. The panel design has been streamlined for ease of use.
- DBV menu panel. The field coloring panel is now opened directly in the menu, but can be detached as a stand-alone panel.
- Multi-bin range specification. A new bin coloring mode features a configurable number of bins, specified by the two endpoints of the range and the midpoint values of each bin. A database cell whose value falls in a given bin is colored by the bin color; i.e. there is no gradient. Cells with values outside the bin range are not colored.
- Gradient and log gradient coloring. The former range/ramp functionality has been updated to use a configurable number of bins, similarly to the multi-bin range specification. Each bin is assigned a color at the bin mid-point, and colors over the range are interpolated. Values outside the range are assigned the colors of the endpoints.
- Automatic range setting. The endpoints of the range and gradient specifications can be automatically detected from the current database field values by pressing the refresh button.
- Undo. New button to undo the last coloring operation.
- Custom. New button for saving the current Color Rule under a custom name, or loading a saved rule.
- Color rule for non-empty cells. non-empty has been added to the Cell coloring options, to apply the coloring specifications to non-empty cells.
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:
- Carbohydrate display has been added as a new 2D mode.
- New Pocket options have been added to the Dock Browser:
- Pocket view. An Enable option enables/disables the pocket view. When disabled, the browsed receptor structure is hidden and made inert.
- Receptor Carbon coloring. A checkbox now enables/disables the Carbon-atom coloring of the receptor. The default color is dark green.
- Ligand render style. New ligand rendering options allow for coloring the ligand (default bright green) and changing the atom/bond display mode. A checkbox enables/disables the ligand atom rendering. The ligand rendering can still be changed using the rendering controls.
- Separate tag for browsed structures. Browsed structures are now assigned their own tag, which is the original tag suffixed by "Browser." When a structure is kept ( or Ligand), the tag reverts to the original.
- Browsed atom set. Browsed structures are now added to the set "Browser Atoms"
- 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:
|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
|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).|
- Correlation Plot. New regression line modes have been
added to the Database Viewer Correlation Plot.
- Quadratic, Logarithmic, Exponential, and Power regression lines are now available.
- New Automatic option chooses the regression line type that best fits the data.
The correlation plot now supports plotting a third and fourth field of data, with the third data field shown using a color range, and the fourth data field shown using size of data points.
- Dihedral Contour Plot. The Dihedral Contour Plot has been
updated. Note that its location in the menus has changed to
- Current angle marker. A set of crosshairs is now displayed in the plot indicating the current dihedral angle value.
- Set dihedral angle from plot. Clicking in the plot will set the dihedral angle in the molecule in MOE.
- Preset dihedral angles. The dihedral angles can be specified in advance by selecting two bonds in the MOE system prior to launching the application.
- Dihedral angle meters in 3D window. Dihedral angle meters are displayed on the molecule in the MOE 3D drawing area to show which dihedral angles are being explored.
- Dihedrals. New button allows to redefine the dihedral angles and update the plot.
- Update. New button to recalculate the plot.
- Export. New button to open the Export panel.
Graphic Object Export. Export of graphic objects via
File formats. Support for the following file formats has been added:
- SDF V3000 enhanced stereochemistry. Support for V3000,
which allows partial and mixed stereochemistry as well as
stereo groups to be specified, has been added. The stereochemical
group types are:
- Absolute (ABS). Absolute configuration is known.
- Relative (OR). Relative configuration among a set of stereo centers is known, but the absolute configuration is not. Thus, the structure represents a single stereoisomer.
- Racemic (AND). Mixture of stereoisomers: a pair of enantiomers or a collection of all diastereomers.
V3000 stereo encoding is supported as follows:
- Enhanced SMILES stereo annotations encode V3000 stereo. V3000 stereo sets, which have number ids, are represented by "@" followed by the number, with the special cases of "@" and "@@" for sets 1 and 2.
- The MOE mdb molecule format has been enhanced to encode V3000 stereo.
- Hybrid-36 format for large PDB files. The base 36 system used to extend residue UID and atom serial numbers beyond the 5-digit limit imposed by the default PDB format is now supported. This system is backward compatible with the standard PDB numbering.
- RCSB Search API v2. MOE has migrated to using Version 2 of the RCSB PDB Search API, which was released on April 13, 2022.
- mmCIF in MOE Projects. MOE project databases now directly support the use of mmCIF files. The RCSB mmCIF distribution is now the primary data source for project databases and the Project Database Update application, with a fallback to PDB files if CIF files are unavailable.
- PDB AMBER22. The AMBER22 option has been added to to use the new AMBER ACE/NME atom naming scheme when writing out PDB files.
- PRMTOP OBC. now writes OBC (igb5) implicit solvent parameters to AMBER PRMTOP files.
Electron Density in applications. DSN6 map and CIF structure factor support have been added to Energy Minimize and Dock.
2D Overlay. Thehas been updated as follows:
- Tag name has been added to the display.
- Attachment points and R-groups are now shown.
- Next and previous buttons wrap when the last or first structure is reached.
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.
- RangeSlider. This new widget provides a double-thumbed
slider representing a value range with a start and stop value.
- Click-dragging between the thumbs will cause both thumbs to be dragged, thus preserving the relative separation between them.
- Mouse wheel or Left-click to the left or the right of the range area moves both thumbs one slider unit.
- Middle-click moves both thumbs, attempting to position the click point in the middle of the range.
- Modifying mouse clicks with the Ctrl key moves the nearest thumb on its own.
- 'sliderValue'. When enabled, displays near the thumbs the values associated with the thumbs. On mouse hover over the values, left-clicking will open a text field in which to set the values explicitly.
Z-clipping () now uses range sliders for both molecule and surface clipping.
- 'scrollbar'. This new value of sliderStyle displays the slider in the style of a scrollbar.
- 'sliderValue'. When enabled, displays near the thumb the value associated with the thumb. On mouse hover over the value, left-clicking will open a text field in which to set the value explicitly.
- Plot Widget. The SVL Plot widget has been updated:
- Line and marker styles. New line (solid-light, 'dashed-light', 'dotted-light') and marker ('round-dot', 'fine-cross') styles have been added.
- 3D and 4D scatter plots. Scatter plots can now display 3- or 4-dimensional series data. The 3d dimension uses a color ramp to qualify the plot points, and the 4th dimension uses size. In the Plot Attributes popup panel, the Z-axis refers to the 3rd dimension, if used, and W-axis the 4th dimension, if used. and
- Logarithmic display. A logarithmic display mode option has been added to the Plot Attributes panel/popup on the Axis tabs.
PSILO Query. The PSILO page of thepanel 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:
- Gaussian g16 c.01
- NAMD 2.14
MOE menus. The following changes have been made to MOE menus.
|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
|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.|
GPU Acceleration. Performance speedups through use of GPU have been realized for the following computations.
- Sidechain packing. The massively parallelizable parts
of the Unary Quadratic Optimization (UQO) techniques used to
efficiently search for best
combinations of rotamers have been reimplemented for GPU.
This results in performance enhancements in:
- Protein Design.
- Homology Model.
- Antibody Modeler.
- Loop Modeler.
- Protein Builder.
- Protein-Protein Dock.
- Protein-Protein Docking. In Protein-Protein Docking, a
coarse-grained bead model is used to reduce the computational
search space. In the coarse-grained minimization
step, the calculation of pairwise bead interaction energies, which
represents a significant amount of the processing time, has been
reimplemented for GPU.
Protein-Protein Docking was additionally sped-up by optimizing its Fast Fourier Transform calculations, used to enumerate all orientations of the "ligand" during pose generation:
- Reduce the number of FFT calculations 24-fold by exploiting rotational symmetries.
- Run multi-threaded FFT calculations.
- New switches. MOE and MOE/batch can be invoked with the
following command-line switches:
- -gpu. Specifies the default GPU device to use. When running -mpu, the GPU to use per worker can be specified.
- -nogpu. Disables GPU usage; calculations will fall back to using just CPU.
- -mpugpu. Machine file worker GPU specification.
- HPC queue submission. The new gpu resource specification keyword is used to specify GPU usage on jobs submitted to job management systems via MOE's HPC framework.
- Precompiled kernels. The GPU kernels for computation are provided as precompiled *.ptx files. This obviates the need for having the CUDA SDK installed locally.
Ensemble Protein Properties. Options have been added to the Protein Properties Residue Table:
- Select. Select in MOE the residues corresponding to the residues selected in the table.
- Color. Color the residues in the Sequence Editor and associated ribbons in MOE by one of the residue properties. The coloring is configurable, with the actually assigned color interpolated between the colors assigned to specifiable maximum positive, zero, and minimum negative property values.
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:
- Build scFv models. Under Sequence, the new scFv option permits building a single-chain Fv by joining two Fv's by a linker (VL-linker-VH, VH-linker-VH), where the linker is part of the query sequence. The resulting scFv fragment can be grafted onto full or fragment antibody templates.
- Custom antibody templates. Through the ab_Model programming interface, build models of any valency or specificity given a custom-built template containing one or more binding domains.
- Grafting Scheme. The CDR definition for grafting purposes has been renamed from "CDR Scheme" to "Grafting Scheme". The CDR residues grafted onto the Fv framework can be collected into a named residue set; note that this collection may be distinct from that of the annotation and numbering of the final model.
- Maximum Number of Framework Models. This new option on the Model tab allows for specifying the number of different framework models to use for building models.
- Annotation. Renaming of the "Residue Numbering" option; this option now controls both residue UIDs and CDR numbering, i.e. the entire antibody sequence will be renumbered, thus providing unique residue UIDs across all Ig domains. IMGT numbering is used for non-Fv regions, and for regions where the chosen scheme does not provide numbering.
Sequence Annotation. IMGT constant domain numbering has been added.
PLIF Analyze.has been updated as follows:
- Ligand display tiles. Ligands are now laid out as a set of ligand tiles that each display properties of the ligand.
- Frequency filter. Filtering on the frequency of fingerprint bits is now configurable using the Frequency filter which has a configurable cutoff.
MOE Projects. The following are updates related to MOE Project Databases:
- Project Search of PSILO databases. Projects served by the PSILO server can now be searched by Project Search. The PSILO projects will be added to the Annotate and Search menus.
- Domain Motif Search of MOE Project databases. can now perform searches on MOE Project databases.
- Support project databases in patch, profile, and custom. Project databases located in MOE "pseudo-roots" are now searchable by Project Search and will be added to the Annotate and Search menus.
- Build from mmCIF files. Project Database Update will preferentially download mmCIF files, from both PSILO and RCSB, for building the project database.
- Project Search Unique Ligand. Unique Ligand has been added to Project Search. When enabled, the result consists of hits containing ligands that do not appear in any other hit in the list.
- Project Search bubbleHelp ligand display. The list of search results in Project Search now provides per-line bubbleHelp in which the ligand is depicted and the ligand name, weight, TPSA, and SLogP values are displayed.
Protein Design. The Protein Design application has been updated as follows:
- Disulfide site enumeration. Multi-site disulfide site enumeration is now available in Disulfide Scan, i.e. Site Limit can be set to >2 (note that the number must be even).
- DBV field coloring of output fields. Field coloring of dStability, dAffinity, and dS-S fields has been added (blue=good, red=bad).
- Layout streamlining. Panel layout has been updated for more intuitive option setting.
- Performance improvements. The dStability calculation has been sped-up, most notably for structures rich in Arginines. Parallel calculation under MPU has also been improved, making more efficient use of available CPUs. Finally, the methodology has been updated to run on available GPU resources, which can result in a significant speed-up of sidechain repacking.
Updated reaction files. Reaction files in MOE have been updated, and are now all in *.rxn format. Applications using reactions have been concomitantly updated:
- Combinatorial Library now reads both *.rxn and *.rdf files. A new Copy Reagent Data option allows data from the input to be written out when saving individual filtered combinatorial reagent databases.
- MedChem Transformations has been updated to read *.rxn files; the use of a database of reactions (as in the former medchem_rxn.mdb) is still supported. Additionally, -2D and -depict command line switches have been added for running batch jobs, corresponding to the UI Generate 2D and Depict options.
- Covalent docking now supports *.rxn files in addition to *.rdf files.
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:
- AMBER Thermodynamic integration.
- Low Mode MD (used e.g. in Conformation Search and Ensemble Protein Properties).
- Saving of AMBER .prmtop files in .
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 ():
|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:
|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. The MOE Sketcher web application now supports reactions and enhanced query annotations.
- Reaction mode. In reaction sketching mode, reactions can be uploaded, displayed, and edited. Import of MOL, RXN, and Reaction SMILES formats are supported.
- Atom mapping. Atom mapping between reagents and products can be generated automatically or specified manually.
- Reaction coloring by component. To more easily visualize the correspondence between reagents and products, reagent atoms that appear in products are highlighted in both reagent and product and colored by reagent color.
- Reaction bond marking. To more easily visualize bonds modified in a reaction, bonds that are broken in the reagent and bonds that are formed in the product are marked with two parallel lines colored according to the reagents involved.
- Title and comment. The sketched reaction can be assigned a title and comment, which will then be displayed.
- Copy/Paste from/to MOE. Direct copy/paste to and from MOE as well as direct mouse drop is supported.
- Enhanced atom query annotation. New atom wildcard and query
properties have been added:
- Elements: H, I
- *: Any
- A: heavy (not H)
- Q: hetero (not C, not H)
- M: any metal
- X: any halogen
- R: unspecified
- Bond count: Implicit hydrogen count + bond count gives total number of neighbours
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:
- Built-in reaction sketcher. Sketch a reaction or browse built-in reactions. The default reactions are located in the folder $MOE/lib/reactions/combi.
- Reaction templates. Built-in reaction templates serve as a starting point for sketching custom reactions.
- Upload reagent catalogs in various formats. Interactive choice of supplier reagents for library enumeration. The supplier databases are automatically searched for reagents matching the reaction.
- Scrollable list of products. Explore any part of the library interactively. Products are calculated and displayed on-the-fly, making the entire library accessible for browsing.
- Set library design goals. Tune the contents of the library by interactive filtering of both reagents and products based on various properties, including molecular properties and common chemical and protective groups.
- Automatic profiling of reagent and product properties. Visualize the distribution of properties in the full library by examining the property histograms in the property filters. The property distribution over the full library is estimated by dynamically accumulating statistics over the growing population of enumerated products; the property distribution is thus available at all times, and becomes increasingly accurate as time progresses.
- Generate a sample of the full library. The sample will have, as much as possible, the same molecular property distribution as the full library, and is generated in an optimal manner to ensure that, even as it is being created, the partial results maximally preserve the library's property distribution.
- Export results. Results can be exported in .sdf or .csv format and include supplier reagent IDs.
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.
- Docking pane. New type of pane featuring a 3D drawing area for visualizing docked poses, and a sidebar in which to choose what to show or hide from view, and where queued or on-going calculations are listed.
- Docking configuration. The docking calculation is set up
. In this page the following
can be specified:
- Upload Receptor. Select or drag'n'drop a .moe file containing the receptor. All docking calculations will be with respect to this common receptor.
- Optionally upload pharmacophore file. A ph4 file can be uploaded.
- Optionally upload docking mdb. Uploading precomputed results precipitates no docking calculations; the poses are displayed in the Dock pane.
- Specify number of parallel jobs. If resources permit, each docking calculation can be run as a separate job submissions.
- Automatically dock structures of interest.
As long as a Docking pane
is shown in the MOEsaic interface, docking calculations
are automatically queued and launched for:
- Highlighted structures
- Selected structures
- Sketched molecules
- Dock information. Information on the dock configuration as well as the currently-running dock jobs can be obtained by hovering over the information icon in the header of the Docking pane tab.
- Multiple Dock panes. Multiple Dock panes can coexist. This will result potentially in multiple concurrent docking calculations.
- Visualize results. The docked poses can be zoomed, rotated, and translated in 3D. Different components of the system can be hidden or shown, and one or more poses can be selected for viewing.
MOEsaic has also been updated with the following enhancements:
- Change pane type. The type of the panes can now be specified. This allows for customization of the MOEsaic window layout, and for the possibility of multiple panes of the same type, thus permitting for example side-by-side comparisons of plots or multiple Dock instances.
- Add multiple virtual compounds. In Sketch mode, the More button allows sketching more than one molecule at a time, and the Add All to Session will result in all virtual compounds being added to the data set at once.
- Display structure fields as depictions on plot axis. To clarify the correspondence between properties calculated on structure data fields and their associated structures, the structures depictions are now displayed in the plot axis area.
- Modify field type. On data set upload, the field types can be adjusted manually.
$MOE/lib files. The following changes have been made to $MOE/lib:
|$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.|
|$MOE/lib/pdbx.xsd.gz||Updated RCSB PDB XML specification.|
|The reaction files included in MOE have been updated as follows:
|$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 $MOE/sample/mol/ are now gzipped.
|$MOE/sample/mol||Examples of pre-docked data files for MOEsaic Dock.|
|$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.|
The following are SVL functions that have been added to or modified in MOE. Please consult the SVL Function Index for more information.
|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
|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.|
|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.|
|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:
|exe_open_shell||The use of this function is no longer supported. exe_open should be used instead.|