Alchemical absolute protein–ligand binding free energies for drug design

By |September 24, 2021|Categories: Publications|Tags: , , |

The recent advances in relative protein–ligand binding free energy calculations [...]

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Perspectives on automated composition of workflows in the life sciences

By |September 7, 2021|Categories: Publications|Tags: |

This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the “big picture” of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years.

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The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

By |September 3, 2021|Categories: Publications|Tags: , |

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers.

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Shape-Restrained Modeling of Protein–Small-Molecule Complexes with High Ambiguity Driven DOCKing

By |August 26, 2021|Categories: Publications|

Small-molecule docking remains one of the most valuable computational techniques [...]

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3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories

By |August 13, 2021|Categories: Publications|Tags: , , , |

3D Representation Sharing (3dRS) is a web-based tool designed to share biomolecular structure representations, including 4D ensembles derived from Molecular Dynamics (MD) trajectories. The server offers a team working in different locations a single URL to share and discuss structural data in an interactive fashion, with the possibility to use it as a live figure for scientific papers. The web tool allows an easy upload of structures and trajectories in different formats.

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