The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
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.
Shape-Restrained Modeling of Protein–Small-Molecule Complexes with High Ambiguity Driven DOCKing
Small-molecule docking remains one of the most valuable computational techniques [...]
3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories
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.
Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue
Molecular docking excels at creating a plethora of potential models [...]
Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling
Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which [...]
ISO 23494: Biotechnology – Provenance Information Model for Biological Specimen and Data.
This project aims to develop a comprehensive W3C PROV based provenance information standard intended for the biomedical research domain.
