New Features
Software Releases
Software Releases
FEP+
- Analyze multi-site protein residue mutations from FEP+ Panel [2021-1]
- ABFEP Web services will now download FMP/FMPdb files with results [2021-1]
- Absolute Binding Free Energy (AB-FEP) functionality is now integrated into FEP+ Panel [2020-4]
- Submit and analyze AB-FEP jobs
- SID Analysis and PDF reports
- Web services submission and downloads
- LiveDesign export of results
- The original “ABFEP Panel (Beta)” will be behind a feature flag, to activate turn on ABFE_CLASSIC_GUI. (The feature flag and the old panel will be removed in 2021-1)
- FEP+ Panel [2020-3]
- Integrated ForceField Builder + FEP Workflow
- Use QuickView to cycle through the edges’ mapping/hotregion data
- Ability to clear all/selected experimental data
- UX improvements to displaying Core SMARTS
- Eliminating redundant SMARTS patterns
- Highlight nodes that match core SMARTS
- GUI support to change # of lambda windows
- ABFEP Panel [2020-3]
- Support for multiple-ligand input
- Web services support
Ligand Alignment
- Save and load ligand alignment interface settings to speed setup of common experiments [2021-1]
- Automatically align macrocycles using a novel tugging-based approach [2021-1]
- Input structure group hierarchy now honored in alignment output [2020-4]
- Users receives warning message if not all ligands could be aligned [2020-4]
- Substructure specification with SMARTS automatically generates SMARTS without H to speed up alignment [2020-4]
- Improve reference ligand specification by allowing to search for it [2020-3]
- Several bug fixes (e.g. tracebacks, job launch failures) [2020-3]
- Smaller default number of generated conformers for jobs based on flex_align to speed up calculation [2020-3]
- Adding tooltip [2020-3]
- Clarification on advanced option specification [2020-3]
- Improved alignments for congeneric series with common scaffolds defined by Bemis-Murcko scaffold or SMARTS [2020-2]
- Improve reference ligand specification [2020-2]
- Update or create new entries for aligned ligands [2020-2]
Force Field
- Significantly improved parameters for charged groups and anisotropic treatment for sulfur in a new version of the force field, OPLS4 [2021-1]
Pharmacophore Modeling
- Perceive pharmacophore features from complex structures and e-pharmacophores when complexes include DNA or RNA [2021-1]
- Simplify application of create_hypoConsensus script which can now read the *.phypo format [2020-3]
Workflows & Pipelining
- KNIME in LiveDesign [2021-1]
- Free file name choice in the Extra file fields and other usability improvements in the two generic protocols
- Model description is updated from the workflow when deployed and models can be sorted by modification date on the admin page
- New LiveDesign model and protocol administration nodes
- Other nodes [2021-1]:
- Supports the latest version of KNIME (v4.3, but includes v4.1.3)
- Includes the biological unit and set the source in the Get PDB node
- The Jaguar minimization node runs on multiple CPUs
- KNIME in LiveDesign [2020-4]
- System specific files and workflow parameters can be changed on the LiveDesign admin page
- Preferences for faster configuration of the Upload as LiveDesign model node
- Surfaces rendering can be controlled and the models deployed to a specific LiveDesign project
- Use nodes from extensions not included in the default installation
- The Prime Build Homology Model node accepts any Parameter flow variable [2020-4]
- Supports the latest version of KNIME (v4.2, but includes v4.1.3) [2020-3]
- Upload as LiveDesign model node [2020-3]
- Generic protocol taking any LiveReport column as input
- Pharmacophore hypotheses can be added to the LiveReport
- The models is created in the specified folder under Computational model
- The protocols and models can be uploaded via a python script
- Option to avoid KNIME version incompatibilities
- Any command line option can be used in the Glide ligand docking node [2020-3]
- The 3D structure type (hence the rendering) and execution mode (automatic/run for each cell) can be controlled in the Upload model to LiveDesign node [2020-2]
- Surfaces and images can be added to the LiveReport [2020-2]
- New Prime Macrocycle Conformation sampling node [2020-2]
- The Molecule reader node takes in cif format [2020-2]
- The Export image to LiveDesign node supports SVG images [2020-2]
Multiple Sequence Viewer
- Read and display custom 1-letter codes from non-standard amino acid libraries [2021-1]
- Finer control of structure alignment via mapping to specific reference chains [2021-1]
- In Dendrogram interface choose desired resolution and export/save image to .pdf and .png formats [2021-1]
- Sequence alignment optimization for homology modeling [2020-4]
- Copy selected sequences and append into existing view tab [2020-4]
- Implemented Consensus Homology Modeling Workflow [2020-4]
- Options to automatically detect and select Heavy or Light chain sequences of antibody [2020-4]
- Allow exporting selected sequences to multiple individual fasta files (1 seq in each file) [2020-4]
Modernized design, new code, new capabilities
- Quick access to MSV from the main Window menu in Maestro or Tasks Menu. Improved user experience through an intuitive, easy to navigate interface that is similar in design to Maestro 11 [2020-3]
- Support for sequence alignment and comparison with options to set alignment method and adjust parameters [2020-3]
- Perform pairwise sequence alignment
- Perform multiple sequence alignment
- Generate a pairwise comparison matrix: compare entire sequences or selected columns based on similarity, identity or conservation
- Layer on and display information from various sources to enhance interpretation of differences or similarities between sequences [2020-3]
- Introduce global annotations
- Apply coloring by property
- View property metrics
- Rapidly and accurately annotate antibody CDR loops
- Rich set of in-buit sequence descriptors can be computed and values displayed in the metrics column next to the sequences.
- Flexibility to upload user-generated descriptors and color sequences by those properties.
- Homology Modeling: Guided step-by-step structure prediction workflows with checkmarks to indicate completed steps [2020-3]
- Find Homologs (BLAST)
- Many types of models are supported
- Simple model: one target, one template
- Chimeric model: one target, multiple templates
- Batch models: multiple targets, one template
- Multichain model: homo- and hetero-multimer
- Smooth integration with 3D structures in the Workspace [2020-3]
- Easily link and unlink sequence to structure
- Align structures based on entire sequence alignment or binding-site alignment
- One-click switching between split and combined chain representations
- Color sequence by structural property
- Apply sequence colors to workspace structure and vice versa
- New heteromultimer homology modeling workflow [2020-2]
- Associating data with sequences: Import per-residue data from experiment or predictions and visualize it mapped onto amino acid sequences [2020-2]
Induced Fit Docking
- Optionally specify additional residues in the binding pocket to be refined [2021-1]
- Force user-specified residues to be mutated and sampled (command line only) [2020-4]
- IFD-MD Speed enhancements of approximately 5X without compromising accuracy [2020-3]
Solubility FEP (Beta)
- Predict the relative solubility of different crystalline morphologies [2021-1]
CryoEM
- Run force field builder as part of a Phenix/OPLS refinement run [2021-1]
- Automated grid scanning of weights and B-factors [2021-1]
- Enable full control over Phenix options in GlideEM [2020-4]
- Automated constraint weight scanning with PHENIX/OPLS3e to determine ideal weights [2020-3]
- PHENIX/OPLS3e - Stability improvements, multi coformer support, support for writing PDB files [2020-3]
Ligand Designer
- Support for non-protein binding sites such as RNA-ligand complexes [2021-1]
- Access the R-Group Creator panel to create custom R-Group libraries [2021-1]
- Up to 7x faster Growth Space performance [2021-1]
- Refined 3D building workflow [2020-4]
- In real-time identify similar purchasable compounds to design ideas. Requires FPsimGPU license sold separately. [2020-4]
- Expanded set of bioisosteres to include nitrogen walks [2020-4]
- Set clash colors for Growth Space [2020-4]
- Improved control of atom picking modes [2020-4]
- Validate and check ligands are congeneric before docking from file [2020-4]
Protein FEP
- Analyze multi-site protein residue mutations from the FEP+ Panel [2021-1]
Ligand Docking
- Provide an estimate of the wall clock time to run the specified Active Learning Glide docking [2021-1]
- Perform billion compound screens quickly with excellent recovery of top-scoring compounds with Active Learning Glide [2020-4]
- Docking ligands in SMILES format from csv/smi inputs with control over ligand preparation settings [2020-4]
- WScore now supports docking macrocycles (command line only) [2020-4]
- Apply shape feature-based constraints in ligand docking with Glide [2020-4]
- Apply Active Learning Glide to dock ultra-large libraries of billions of compounds using a combination of machine learning and Glide docking beta [2020-3]
- In MCS docking interface select to use flexible ligand alignment or produce docking-only alignments [2020-2]
- Dock from SMILES formats directly (*.smi or *.csv) with Glide to streamline virtual screening and facilitate large library screening [2020-2]
Protein Preparation
- New Protein Preparation Workflow in Beta [2021-1]
Maestro Graphical Interface
- Quickly select atoms in the Antibody-Antigen interface [2021-1]
- Support “Drag & Drop” into Maestro for all readable file formats (excluding Projects) [2021-1]
- Use the native file dialog on Windows for increased performance [2021-1]
- New “Workflow Action Menu” (WAM) [2020-4]
- Serves as a “mini” Tasks menu on the Project Table and Entry List offering only the recommended application panels for a given group e.g. results from a previously run calculation.
- 20-4 WAM supports: pose viewer docking results, hypotheses data, AutoTS energetics, residue scanning, and numerous Materials Science workflows.
- Finer control over ligand detection preferences [2020-4]
- Export project table data, including 2D images to an Excel spreadsheet [2020-4]
- Export view of 2D viewer to single or multiple images [2020-4]
- Build Biopolymer from Sequence [2020-4]
- Optionally grow 5’ to 3’ or 3’ to 5’ DNA/RNA chains
- Support for single-stranded RNA and double-stranded RNA A-helix
- Send Project Scenes to PyMOL [2020-4]
- Possibility to align simulation cell with workspace axes [2020-4]
- Mouse Actions: Add "Translate (& spot center)" to PyMOL mode [2020-4]
- Add 3D cursor to Looking Glass workspace [2020-4]
- Get PDB Dialog: Add support for CIF downloads [2020-4]
- Rapidly and easily perform manual or guided lead optimization with the Ligand Designer [2020-3]
- “Design your way” with automatic prediction of protein-ligand complex geometry
- Whiteboard-like design in 2D
- Design ligands in 3D without protein
- Design ligands in 3D with simple view of protein interactions
- Design in full 3D with protein
- Overlay information critical to design
- See regions of the binding pocket available for ligand growth
- View protein ligand interactions including clashes
- View protein and ligand surfaces
- View replaceable and displaceable water sites identified by WaterMap
- Recognize ligand bonds amenable to common medicinal chemistry reactions
- Guided workflows speed design
- Bioisostere replacement
- Isostere scanning
- Replace or displace water sites
- Form additional protein-ligand interactions
- Cyclize ligands
- Hybridize ligands (merge R-groups)
- Dock ligands from file
- Tailor chemistry to your project with custom R-group libraries and property filters
- Quickly assess molecular suitability with property-based radar plot (MW, logP, HBA, HBD, PSA). Add user properties from the PT.
- Send favorite designs for rank ordering by affinity with FEP+, for post-processing and dissemination in LiveDesign, or to Excel
- “Design your way” with automatic prediction of protein-ligand complex geometry
- Faster rendering performance for the Looking Glass Holographic Display [2020-3]
- Resize the 2D Overlay [2020-3]
- Allow selection of residues at the protein-membrane interface [2020-3]
- 3D Builder: Build DNA and RNA Strands from Sequence [2020-3]
- Rapidly and easily perform manual or guided lead optimization with the Ligand Designer now in open beta [2020-2]
- “Design your way” with automatic prediction of protein-ligand complex geometry
- Whiteboard-like design in 2D
- Design ligands in 3D without protein
- Design ligands in 3D with simple view of protein interactions
- Design in full 3D with protein
- Overlay information critical to design
- See regions of the binding pocket available for ligand growth
- View protein-ligand interactions including clashes
- View protein and ligand surfaces
- View replaceable and displaceable water sites identified by WaterMap
- Recognize ligand bonds amenable to common medicinal chemistry reactions
- Guided workflows speed design
- Bioisostere replacement
- Isostere scanning
- Replace or displace water sites
- Form additional protein-ligand interactions
- Cyclize ligands
- Hybridize ligands (merge R-groups)
- Tailor chemistry to your project with custom R-group libraries and property filters
- Quickly assess molecular suitability with property-based radar plot (MW, logP, HBA, HBD, PSA)
- Send favorite designs for rank-ordering by affinity with FEP+, for post-processing and dissemination in LiveDesign, or to Excel
- “Design your way” with automatic prediction of protein-ligand complex geometry
- Support for Looking Glass Holographic Display [2020-2]
- Allow selection of residues involved in interactions [2020-2]
- Easily set measurements via the right-click context menu. [2020-2]
Desmond Molecular Dynamics
- Perform protein and ligand RMSF Analyses in Trajectory Plots interface [2021-1]
Ligand Preparation and Conformation Generation
- Prepare ligands with up to 500 atoms through the interface [2021-1]
Quantum Mechanics
- Molecular orbital coefficients are printed in the canonical orbital space via new keyword ip108 [2021-1]
- Automatically align theoretical and experimental vibrational circular dichroism (VCD) spectra in the Spectrum Plot panel [2021-1]
- New basis sets d-aug-cc-pvdz/tz and t-aug-cc-pvdz/tz [2021-1]
- New DFT functionals GLYP, revTPSS, revTPSSh, SOGGA11-X, KT2, MGGA-MS0, MGGA-MS1, MGGA-MS2, MGGA-MS2h, and ωB97M-V [2021-1]
- Six new DFT functionals have been added: TPSSh, MN12-SX, SCAN0, G96, RPBE, revPBE [2020-4]
- The definitions of BHandH as well as BHandHLYP functionals now agree with those used by other QM programs [2020-4]
- Ring-chain tautomers can be generated and scored from the QM Conformer and Tautomer Predictor Panel [2020-4]
- Methanol, ethanol, acetonitrile, and DMSO solvents are supported in conformational search built into the VCD and ECD workflow [2020-4]
- Command-line only
- MacroModel conformational search is performed either in water or chloroform, but subsequent DFT optimization is performed in methanol, ethanol, acetonitrile, or DMSO
- Polarizability is now added to Project Table properties [2020-4]
- The sarc-zora basis is updated to include Actinides [2020-4]
- Mössbauer spectroscopy [2020-3]
- Optionally use robust peaks when aligning VCD spectra with spectrum_align.py [2020-3]
- Compute thermochemical properties at a range of pressures [2020-3]
- Ring-chain tautomers can now be generated and scored in the AutoConf.py workflow [2020-3]
- .cosmo files for COSMO-RS calculations [2020-3]
- Batch calculations launched from the command line now optionally output and group failed subjobs to simplify their further processing [2020-3]
- Easily search, filter, and select from a large number of functionals and basis sets [2020-2]
- New functionals TPSS, SCAN, PKZB, SOGGA, SOGGA11, BOP [2020-2]
- Becke-Johnson’s and Sherrill’s dispersion corrections D3(BJ), D3M, and D3M(BJ) are available for a number of functionals [2020-2]
- Spectrum Plot panel can now visualize Jaguar-computed Raman spectra [2020-2]
- Script qm_descriptors.py which outputs QM descriptors now also outputs relative/absolute NMR shifts, Stockholder charges, and NBO charges [2020-2]
- Analytic NLO-V basis set optimized for polarizability calculations is available [2020-2]
- Maximum number of iterations in PBF implicit solvent calculations can be controlled by the keyword maxpbfit [2020-2]
- 1D/2D distributed_scan.py jobs output a .grd file even if some subjobs fail [2020-2]
- NMR chemical shifts are available for a number of dispersion-corrected functionals [2020-2]
Empirical and QM-based pKa Prediction
- Improved selection of pKa atoms in the Jaguar pKa panel [2020-4]
- Allow regular and customized OPLS3e force field for conformational search in Jaguar pKa [2020-3]
AutoQSAR
- Enable one to only use user-provided descriptors from the Project Table or uplodated by file [2020-4]
Mixed Solvent MD (MxMD)
- Support for nucleic acid-based (DNA and RNA) solutes [2020-4]
- Include probe structures that match each hotspot [2020-3]
Cheminformatics
- Include script to perform feature selection (feature_selection.py) [2020-4]
- Create and apply Kohonen Self Organizing Maps from Canvas fingerprints or properties - beta [2020-3]
- Create and apply individual categorical and continuous QSAR models with full control over the features applied and machine learning - beta [2020-3]
- Create and make predictions with kPLS, MLR, PCR, Bayes or Recursive Partitioning machine learning techniques
- Employ a broad range of Canvas fingerprints, atomic and molecular descriptors, or user provided descriptors to create machine learning models
- Visualize atomic contributions from kPLS model predictions
- Automatic or manual creation of test/training set splits
Shape Screening
- Run CPU-based queries against Phase hypothesis features stored in *.phypo files including use of excluded volume specification [2020-4]
- Split a GPU Shape bin file into multiple files for processing in parallel across multiple GPUs [2020-2]
OPLS3e Force Field
- Schrodinger-ANI options to speed up fitting used by default and available via the FFB GUI [2020-3]
- FFBuilder integration of the Schrodinger-ANI neural network for 2X faster fitting (command line only) [2020-2]
Protein Homology Modeling
- Support for increased control of minimization parameters in all Prime refinement jobs ( loop predictions, sidechain predictions, binding site optimization etc) from the command-line [2020-3]
Enumeration
- Improved reaction search by name by including description and name [2020-3]
Covalent Ligand Docking
- Apply user-defined constraints throughout refinement step [2020-3]
- Support for attachment atoms containing ‘ in the atom name ( ie nucleic acids) [2020-3]
Binding Site Characterization
- Perform kinase binding site residue conservation analysis via new kinase_conservation_analysis.py script [2020-3]
- Returns pairs of residues that are unique enabling optimization of small molecules for selectivity
- Atom level properties annotate pairs of residues which are most unique across the gene family
Molecular Dynamics
- Removal of Desmond CPU [2020-3]
QM/MM (QSite)
- QSite now supports the OPLS3e force field [2020-3]
- Dispersion-corrected functionals are now supported in the hydrogen-cap model [2020-2]
- The setting qsite_ff = opls3e in QSite input file activates OPLS3e [2020-2]
Macrocycles
- Optionally provide inputs to macrocyclization script by input file [2020-3]
- Generate fusion protein peptide-linkers designs, ADC linkers, and fuse dimeric ligands with ability link disconnected molecules (command line only) [2020-3]
- Optionally provide inputs to macrocyclization script by input file [2020-2]
- Generate fusion protein peptide-linkers designs, ADC linkers, and fuse dimeric ligands with ability link disconnected molecules (command line only) [2020-2]
FPsim-GPU
- Easily select or deselect all databases [2020-2]