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AFITT-CL v2.1.0 released

Mon, 07/11/2011 - 15:47 — admin
AFITT-CL v2.1.0 has been released. This is the first release of the AFITT command line utilities that fully support fragment and cocktail fitting to crystallographic data. In addition, poses fit to density can be re-ranked based on various docking scores (PLP, Chemscore). This is quite useful when analyzing highly symmetric ligands that can be fit to density equally well with multiple poses.

AFITT-CL is a command line application to help crystallographers fit ligands to observed data. Ligands are placed in density and optimized in real-space limiting molecular strain thereby producing excellent matches to density while preserving known chemistry. A high quality flexible refinement dictionary is generated for the fit ligand or the protein-ligand complex for use in subsequent refinement with Refmac5 or CNX.

AFITT-CL is available for download now. Existing licenses will continue to work. If a new license is needed, please contact your account manager or business@eyesopen.com to request a new one.

 

AFITT-CL 2.1.0 FEATURES

FLYNN
  • FLYNN now sorts the output fits based on real space correlation coefficient if applicable (RSCC)
  • FLYNN now can automatically fit fragment cocktails. (use -fragment flag)
  • FLYNN adds additional scores to all ligands besides the default MMFF Tanimoto/Shape, these are RSCC (Real space correlation coefficient), PLP (Piecewise-linear potential, requires protein) and Chemscore (requires protein).
  • -resname now forces the ligand to use the given residue name even if it conflicts with the internal monomer library.
  • chainid Output the ligands with the given chain id.
WRITEDICT
  • Updated internal REFMAC and RCSB to current versions.
  • When remapping dictionaries, WRITEDICT now indicates where the matching monomer was sourced.
  • Moved "lookup" out of the -strict settings to a new flag "-lookup" adding this switch will search for a matching monomer from the internal libraries using the current -strict settings.
  • -force options added. WRITEDICT will output the residue name even if it doesn't match the internal list of known monomers.
  • Various corrections to aniline nitrogen dictionaries.

RESOURCES

About OpenEye Scientific Software

OpenEye Scientific Software Inc. is a privately held company headquartered in Santa Fe, New Mexico, with offices in Boston, Massachusetts, Strasbourg, France and Tokyo, Japan. It was founded in 1997 to develop large-scale molecular modeling applications and toolkits. Primarily aimed towards drug discovery and design, areas of application include:

The software is designed for scientific rigor, as well as speed, scalability and platform independence. OpenEye makes most of its technology available as toolkits - programming libraries suitable for custom development. OpenEye software typically is distributable across multiple processors, supports 64-bit processing, and runs on Linux, Windows and Mac OS X. For further information on the company and its products, see www.eyesopen.com

For additional information
Joseph Corkery, M.D.
Vice President, Business Development
+1-505-473-7385 x76
Email: business@eyesopen.com