Software
BioExcel Building Blocks (BioBB’s) are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments.
The MDDB Workflow is a tool that standardizes, validates, and analyzes molecular dynamics projects by converting raw simulation outputs into normalized structure and trajectory files and running automated QA and analysis pipelines. The workflow is designed to run reproducibly on a laptop, in containers, or on HPC systems, supporting multiple input formats, automated checks, and flexible deployment.
CGeNArate is a new model for molecular dynamics simulations of very long segments of B-DNA in the context of biotechnological or chromatin studies. The developed method uses a coarse-grained Hamiltonian with trajectories that are back-mapped to the atomistic resolution level with extreme accuracy by means of Machine Learning Approaches. CGeNArate, a new model for molecular dynamics simulations of very long segments of B-DNA in the context of biotechnological or chromatin studies. The developed method uses a coarse-grained Hamiltonian with trajectories that are back-mapped to the atomistic resolution level with extreme accuracy by means of Machine Learning Approaches.
BioExcel Building Blocks (BioBB’s) are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments.
The MDDB Workflow is a tool that standardizes, validates, and analyzes molecular dynamics projects by converting raw simulation outputs into normalized structure and trajectory files and running automated QA and analysis pipelines. The workflow is designed to run reproducibly on a laptop, in containers, or on HPC systems, supporting multiple input formats, automated checks, and flexible deployment.
CGeNArate is a new model for molecular dynamics simulations of very long segments of B-DNA in the context of biotechnological or chromatin studies. The developed method uses a coarse-grained Hamiltonian with trajectories that are back-mapped to the atomistic resolution level with extreme accuracy by means of Machine Learning Approaches. CGeNArate, a new model for molecular dynamics simulations of very long segments of B-DNA in the context of biotechnological or chromatin studies. The developed method uses a coarse-grained Hamiltonian with trajectories that are back-mapped to the atomistic resolution level with extreme accuracy by means of Machine Learning Approaches.
Websites
BioBB (BioExcel Building Blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. In this site we provide the ability of running several workflows on top of the BioBB’s. Workflows can be run starting from a structure, a DNA sequence, a trajectory, a protein+ligand complex or a small molecule.
CGeNArate is an intuitive environment for simulation of both unconstrained and constrained DNA, such as circular DNA and protein-DNA simulations. The simulations are obtained using CGeNArate, a new model for molecular dynamics simulations for B-DNA in the context of biotechnological or chromatin studies.
BIGNASim is a comprehensive platform including a database system and an analysis portal, aimed to be a general database for handling nucleic acids simulations. BIGNASim allows direct access to individual trajectory data and pre-computed analyses, as well as global analyses performed on the whole database.
The 3-dimensional structure Representation Sharing (3dRS) web application has been built with the aim of sharing visualizations of 3D biological structures through the web. In these visualizations, users will be able to draw several representations with different selections of the structure(s) previously uploaded to the application.
The hexABC project is the latest effort (2021) of the Ascona B-DNA (ABC) Consortium. The study is focused on the systematic characterization of the physical properties of all 2080 unique hexanucleotides, from a collection of 380, 10μs-long MD simulations. The vast simulation effort will allow the exploration of long-term dynamics of solvated duplexes to define potential frustration effects in DNA, sequence-dependent solvent and ion atmosphere, correlation and signal transfer effects, which could not be explored in previous calculations focussed in much shorter elements.
BioBB (BioExcel Building Blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. In this site we provide the ability of running several workflows on top of the BioBB’s. Workflows can be run starting from a structure, a DNA sequence, a trajectory, a protein+ligand complex or a small molecule.
CGeNArate is an intuitive environment for simulation of both unconstrained and constrained DNA, such as circular DNA and protein-DNA simulations. The simulations are obtained using CGeNArate, a new model for molecular dynamics simulations for B-DNA in the context of biotechnological or chromatin studies.
BIGNASim is a comprehensive platform including a database system and an analysis portal, aimed to be a general database for handling nucleic acids simulations. BIGNASim allows direct access to individual trajectory data and pre-computed analyses, as well as global analyses performed on the whole database.
The 3-dimensional structure Representation Sharing (3dRS) web application has been built with the aim of sharing visualizations of 3D biological structures through the web. In these visualizations, users will be able to draw several representations with different selections of the structure(s) previously uploaded to the application.
The hexABC project is the latest effort (2021) of the Ascona B-DNA (ABC) Consortium. The study is focused on the systematic characterization of the physical properties of all 2080 unique hexanucleotides, from a collection of 380, 10μs-long MD simulations. The vast simulation effort will allow the exploration of long-term dynamics of solvated duplexes to define potential frustration effects in DNA, sequence-dependent solvent and ion atmosphere, correlation and signal transfer effects, which could not be explored in previous calculations focussed in much shorter elements.