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• date: 23 March 2023
• posted by: voska89

BioSolvetIT SeeSAR 12 what's new
Narcissus provides users with the possibility to perform ligand-based drug discovery (LBDD) with the new Similarity Scanner Mode. The underlying algorithm FlexS aligns compounds based on their shape and molecular functionalities allowing virtual screening approaches even when no target structure is available.
Furthermore, we improved molecule management in the tables for fast and convenient processing of poses and results.
SeeSAR 'Narcissus' was apparelled with a novel, powerful tool for lightning-fast pocket exploration: FastGrow. Fastgrow uses a novel, fast, and accurate shape-based algorithm for structure-based growing into binding pockets. Users can screen tens of thousands of fragments within seconds to receive an optimized suggestion that complements the binding site. Application scenarios of FastGrow involve fragment-based growing approaches, group replacement to improve affinity, scaffold hopping towards particular binding motives of interest (e.g., a hinge binding motif), screening of pocket filling groups to increase selectivity, compound library generation, and many more.
Further, we added several other augmentations to provide users with more options to guide the outcomes of results (e.g. handling of six-membered rings).

Introduction of FastGrow to the Inspirator Mode
- The existing growing algorithm of SeeSAR has been replaced by FastGrow. Fastgrow uses a novel, fast, and accurate shape-based algorithm for structure-based growing into binding pockets. Users can screen tens of thousands of fragments within seconds to receive an optimized suggestion that complements the binding site. SeeSAR features a library of 12,000 fragments for growing per default, and a larger, more diverse library with 120,000 is available as download.
- Please note that following pharmacophore constraints cannot be used with FastGrow calculations: Donor acceptor interaction contact, Donor interaction contact, My own SMARTS, and Covalent warhead.
Enhancements to the Docking Mode
- Users can now control the allowed conformations of six-membered rings via an additional slider in the pose generation parameters menu.
- The .flexx docking definition file exported from SeeSAR now also takes the number of poses value set in SeeSAR.
- The user-selected value of the allowed six-member ring conformations is also taken into the .flexx definition file exported from SeeSAR.
Enhancements to the Similarity Scanner
- Users can now control the allowed conformations of six-membered rings via an additional slider in the Similarity Scanner parameters menu.
- The .flexs definition file exported from SeeSAR now also takes the number of poses and minimum similarity rating values set in SeeSAR.
- The user-selected value of the allowed six-member ring conformations is also taken into the .flexs definition file exported from SeeSAR.
Ligand highlights
- If a PDB file loaded into SeeSAR has the "subject of investigation" / "ligand of interest (LOI)" annotation in its entry, it is now indicated via an additional "LOI" column in the ligand extraction step.
- Users can control the number of solutions to be generated in the Inspirator Mode via a slider mechanism.
- Users are directly informed that larger fragment files can be downloaded either directly or at a later point of time in the Inspirator Mode.
- Molecules pushed between modes retain the 3D visibility setting and user-defined colors.
- SeeSAR now features a ReCore index with 20,000 fragments per standard.
- After the first execution of a ReCore run in the Inspirator Mode, a "give me more solutions!" button shows up, informing the user that more solutions are available.

BioSolvetIT SeeSARallows drug designers to work with molecules interactively, for example, by docking ligands into the active sites of proteins to optimize hits. This interactive tool has been conceived to be easy to use, and will assist you in calculating physico-chemical properties, affinity estimations, and on-the-fly editing and hypothesis testing. You will learn how to optimize the tightness of fit and create meaningful graphics.
What's new in SeeSAR 12 (Narcissus)
BioSolveIT GmbHis a Bio- and Cheminformatics company. Its core businesses are software, services, and research collaborations. With three founders in academia, BioSolveIT has its backbone in research and catalyzes the genesis of products off of basic research successes. Best known is its molecular docking software FlexX. With the FTrees program BioSolveIT took leadership in ultra-fast virtual high throughput screening using a fragment reassembly based approach.






   
   
   

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