Dataset Information

Pywindow: Automated Structural Analysis of Molecular Pores.

ABSTRACT: Structural analysis of molecular pores can yield important information on their behavior in solution and in the solid state. We developed pywindow, a python package that enables the automated analysis of structural features of porous molecular materials, such as molecular cages. Our analysis includes the cavity diameter, number of windows, window diameters, and average molecular diameter. Molecular dynamics trajectories of molecular pores can also be analyzed to explore the influence of flexibility. We present the methodology, validation, and application of pywindow for the analysis of molecular pores, metal-organic polyhedra, and some instances of framework materials. pywindow is freely available from github.com/JelfsMaterialsGroup/pywindow .

SUBMITTER: Miklitz M

PROVIDER: S-EPMC6307083 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

pywindow: Automated Structural Analysis of Molecular Pores.

Miklitz Marcin M Jelfs Kim E KE

Journal of chemical information and modeling 20180921 12

Structural analysis of molecular pores can yield important information on their behavior in solution and in the solid state. We developed pywindow, a python package that enables the automated analysis of structural features of porous molecular materials, such as molecular cages. Our analysis includes the cavity diameter, number of windows, window diameters, and average molecular diameter. Molecular dynamics trajectories of molecular pores can also be analyzed to explore the influence of flexibil ...[more]

PMID: 30199639

Similar Datasets

Project description:Summary Membrane proteins are central to many pathophysiological processes, yet remain very difficult to analyze structurally. Moreover, high-throughput structure-based drug discovery has not yet been exploited for membrane proteins because of lack of automation. Here, we present a facile and versatile platform for in meso membrane protein crystallization, enabling rapid atomic structure determination at both cryogenic and room temperatures. We apply this approach to human integral membrane proteins, which allowed us to identify different conformational states of intramembrane enzyme-product complexes and analyze by molecular dynamics simulations the structural dynamics of the ADIPOR2 integral membrane protein. Finally, we demonstrate an automated pipeline combining high-throughput microcrystal soaking, automated laser-based harvesting, and serial crystallography, enabling screening of small-molecule libraries with membrane protein crystals grown in meso. This approach brings needed automation to this important class of drug targets and enables high-throughput structure-based ligand discovery with membrane proteins. Graphical abstract Highlights • A platform for rapid in meso structures by serial crystallography (SSX)• Insights into ADIPOR2 receptor-ligand dynamic interactions• A web-based application for remote user-guided experimental design and execution• An automated SSX-based ligand discovery pipeline for membrane proteins is introduced Motivation Membrane proteins are key regulators of most physiological processes and represent attractive targets for drug discovery programs. One of the most successful methods to obtain high-resolution structures of membrane proteins relies on in meso crystallization in combination with serial synchrotron crystallography. However, this remains a difficult process, with challenges at every step, including complex manual sample recovery protocols leading to limited throughput and sample loss and the difficulty in carrying out high-throughput ligand screening experiments. We have developed a new approach enabling rapid, automated structural analysis of membrane proteins in meso based on the CrystalDirect technology that addresses these issues, enabling high-throughput drug discovery with membrane proteins. Membrane proteins control many biological processes and represent attractive targets for drug discovery, but are difficult to study structurally. Healey et al. present an automated approach, combining the CrystalDirect technology and serial crystallography, for rapid structural analysis of membrane proteins and opening new opportunities for high-throughput drug discovery.

Dataset Information

Pywindow: Automated Structural Analysis of Molecular Pores.

Publications

pywindow: Automated Structural Analysis of Molecular Pores.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure