• Energy minimization of proteins and protein-ligand complexes in the Protein Editor mode with 17 force fields to pick from and the AutoSMILES method parameterizing small molecules without the need for manual intervention. The minimized proteins are saved as additional entries to the Protein Editor table.
  
• The minimization can be done in two levels of flexibility with the user being given the choice of having the backbone fixed and sidechains flexible for minimization, or the entire protein including the backbone to be minimized.
  
• The minimization can optionally be GPU-accelerated given the availability of a compatible GPU. The usage of the GPU can be explicitly configured via the System Settings in SeeSAR.
  
• The minimization involves several clean-up steps including the completion of incomplete residues in the structure (absent sequence segments are not covered or completed by this step).
  

• Successful operation of remote docking operations including Space Docking in SeeSAR 14.1 requires upgrading to HPSee 2.1.
  
• Results returned from server are now sorted by LE by default to avoid the size of fragments biasing the results when sorted by affinity. This change of default is exclusive to the C-S-D mode.
  
• New visual guidance for the selection of fragments for extension after the anchoring step has been introduced. Whether the extension can happen in either two possible directions or in several possible directions around the linker atom is visually represented by either arrows or circular highlighting in the 3D visualization respectively.
  
• It is now possible to stop and restart an already running C-S-D step at any point of time so that configuration errors made on the step can be fixed immediately without having to abandon the current workflow and start a new one.
  
• It is now possible to reconnect to a HPSee server if the connection was lost at some point during execution due to common causes like power failure or loss of connectivity to the network. A "reconnect" button that appears on the interface in such situations can be clicked to attempt reestablishing the connection to the server.
  
• The interface of the LE and LLE filters in the C-S-D mode has been changed from a button-based interaction to a slider-based interaction to overcome previous limitations in fetching data when non-consecutive combinations of buttons are clicked.
  

• Red/black lines indicate unresolved segments that occur within binding sites of proteins indicating the criticality of the missing segments for any downstream workflows such as docking and scoring.
  
• The visualization can be toggled on/off via a newly added button in the Visualization settings.
  

• SeeSAR 14.1 brings significant improvements in cross-platform consistency for docking and scoring workflows.
  
• A new molecular descriptor/property namely, "Maximum number of consecutive rotatable bonds" has been introduced in SeeSAR to enable sorting and filtering of molecules based on conformational flexibility as implied by this property.
  
• Molecules from a mode can now be added to other modes like the Docking Mode and Similarity Scanner as "references" and not "templates".
  
• A molecule added as reference to the Docking Modes can be either used as a "template" to guide the docking when the "template docking" button is clicked, and is considered as a "visual reference" when the "standard docking" button is clicked. This behavior applies to the local, external and the Space Docking Mode.
  
• All numeric properties that are available for filtering in the Analyzer can now be viewed by switching the respective columns in all modes that have molecule tables to enable sorting of datasets based on these properties.
  
• Protein-ligand complexes from a mode can be transferred to the Protein Editor either via the context menu on individual entries or by checking multiple entries and adding them to the toolbar via the toolbar button. To edit or minimize one of the proteins added via this mechanism, the entry must be added again to the Protein Editor via the context menu to bring it to the edit state.
  
• .cif and .mcif files can now be associated with SeeSAR as the default program to open these files by directly double clicking on them, similar to how it is with .pdb files.
  
• When a SeeSAR project cannot be opened, the user now gets a more informative explanation about the potential reasons (e.g., version incompatibility or file corruption) as to why the project cannot be opened.
  

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