MIMUMBA Revisited: Torsion Angle Rules for Conformer Generation Derived from X-ray Structures

نویسندگان

  • Jens Sadowski
  • Jonas Boström
چکیده

A method has been developed which automatically generates SMARTS patterns for four-atomic torsional fragments, searches experimental structures in the Cambridge Crystallographic Database, and obtains rules for preferred torsion angles in drug-size molecules. These rules can be used for exhaustive conformational analysis using the popular conformer generator OMEGA. This approach results in an overall improvement of quality and coverage of conformational space when comparing conformer ensembles generated by this method with results obtained by using the default OMEGA setup. In particular, the percentage of structures with at least one conformation closer than 0.5 A to the X-ray structure improves from 84% to 92% in a test set of 11 027 experimental structures from the CSD. Moreover, the average RMS distance of the closest conformation to the X-ray structure improves from 0.30 to 0.22 A.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Systematic search for pairwise dependencies of torsion angles

Most available tools for conformer generation, like OMEGA [1], ROTATE [2], and MIMUMBA [3], divide the conformational space into quantized degrees of freedom, i.e. torsion angles, which are treated independently. The independence of torsions is however not valid for all fragments [4]. There are pairs of mutually dependent degrees of freedom e.g. two consecutive torsion angles in aryl-X-aryl sys...

متن کامل

PubChem3D: Conformer generation

BACKGROUND PubChem, an open archive for the biological activities of small molecules, provides search and analysis tools to assist users in locating desired information. Many of these tools focus on the notion of chemical structure similarity at some level. PubChem3D enables similarity of chemical structure 3-D conformers to augment the existing similarity of 2-D chemical structure graphs. It i...

متن کامل

Torsion angle dynamics for NMR structure calculation with the new program DYANA.

The new program DYANA (DYnamics Algorithm for Nmr Applications) for efficient calculation of three-dimensional protein and nucleic acid structures from distance constraints and torsion angle constraints collected by nuclear magnetic resonance (NMR) experiments performs simulated annealing by molecular dynamics in torsion angle space and uses a fast recursive algorithm to integrate the equations...

متن کامل

Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures.

Statistical potentials that embody torsion angle probability densities in databases of high-quality X-ray protein structures supplement the incomplete structural information of experimental nuclear magnetic resonance (NMR) datasets. By biasing the conformational search during the course of structure calculation toward highly populated regions in the database, the resulting protein structures di...

متن کامل

Fluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction.

Protein molecules exhibit varying degrees of flexibility throughout their three-dimensional structures. Protein structural flexibility is often characterized by fluctuations in the Cartesian coordinate space. On the other hand, the protein backbone can be mostly defined by two torsion angles ϕ and ψ only. We introduce a new flexibility descriptor, backbone torsion-angle fluctuation derived from...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:
  • Journal of chemical information and modeling

دوره 46 6  شماره 

صفحات  -

تاریخ انتشار 2006