Dataset Information

BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping.

ABSTRACT: Small molecule flexible alignment is a critical component of both ligand- and structure-based methods in computer-aided drug discovery. Despite its importance, the availability of high-quality flexible alignment software packages is limited. Here, we present BCL::MolAlign, a freely available property-based molecular alignment program. BCL::MolAlign accommodates ligand flexibility through a combination of pregenerated conformers and on-the-fly bond rotation. BCL::MolAlign converges on alignment poses by sampling the relative orientations of mutually matching atom pairs between molecules through Monte Carlo Metropolis sampling. Across six diverse ligand data sets, BCL::MolAlign flexible alignment outperforms MOE, ROCS, and FLEXS in recovering native ligand binding poses. Moreover, the BCL::MolAlign alignment score is more predictive of ligand activity than maximum common substructure similarity across 10 data sets. Finally, on a recently published benchmark set of 20 high quality congeneric ligand-protein complexes, BCL::MolAlign is able to recover a larger fraction of native binding poses than maximum common substructure-based alignment and RosettaLigand. BCL::MolAlign can be obtained as part of the Biology and Chemistry Library (BCL) software package freely with an academic license or can be accessed via Web server at http://meilerlab.org/index.php/servers/molalign .

SUBMITTER: Brown BP

PROVIDER: S-EPMC6598199 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Publications

BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping.

Brown Benjamin P BP Mendenhall Jeffrey J Meiler Jens J

Journal of chemical information and modeling 20190212 2

Small molecule flexible alignment is a critical component of both ligand- and structure-based methods in computer-aided drug discovery. Despite its importance, the availability of high-quality flexible alignment software packages is limited. Here, we present BCL::MolAlign, a freely available property-based molecular alignment program. BCL::MolAlign accommodates ligand flexibility through a combination of pregenerated conformers and on-the-fly bond rotation. BCL::MolAlign converges on alignment p ...[more]

PMID: 30707580

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Project description:BackgroundAvailable research about the anatomic patterns of intertrochanteric fractures is lacking, and fracture mapping has not previously been performed on intertrochanteric fractures. This study aimed to determine the major trajectories of intertrochanteric fracture lines using computed tomography data from a series of surgically treated patients.MethodsIn this study, 504 patients with intertrochanteric fractures were retrospectively analyzed. Fracture patterns were graded according to Arbeitsgemeinschaft für Osteosynthesefragen (AO) classification. Fracture lines were transcribed onto proximal femoral templates and graphically superimposed to create a compilation of fracture maps that were subsequently divided into anterior, posterior, lateral, and medial fracture maps to create a three-dimensional (3D) pattern by reducing fragments in the 3D models. The fracture maps were then converted into frequency spectra. The major fracture patterns were assessed by focusing on the lateral femoral wall, lesser trochanter, intertrochanteric crest, and inner cortical buttress.ResultsAnterior, posterior, lateral, and medial fracture maps were created. The majority of fracture lines (85.9%, 433/504) on the anterior maps were along the intertrochanteric line where the iliofemoral ligament was attached. In the medial plane, the majority of fracture lines (49.0%, 247/504) shown on the frequency spectrum included the turning point involving the third quadrant. In the posterior plane, the majority of fracture lines (52.0%, 262/504) involved the intertrochanteric crest from the greater to the lesser trochanter. In the lateral plane, the majority of fracture lines (62.7%, 316/504) involved the greater trochanter at the gluteus medius attachment.ConclusionsThe fracture patterns observed in the present study might be used to describe morphologic characteristics and aid with management strategies. Further classifications or modifications that incorporate the fracture patterns identified in this study may be used in future research.

Dataset Information

BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping.

Publications

BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping.

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