Liife sciences data pertain to the following six themes:

 

 

Modeling and Molecular Dynamics (MD)

study of important drug targets: existing and generated datasets for further analysis, e.g. MD trajectories of oncogenic proteins with mutations relevant to the SEEM area), Workflows for simulating a protein with commonly-used codes (e.g. NAMD, GROMACS), repository of analysis tools for MD trajectories.

Computer-aided drug design (CADD)

Databases of interesting targets for CADD relevant to the SEEM region, Existing and generated datasets for further analysis (describe), Workflows for CADD with commonly used programs (e.g. Glide, Autodock), Workflows/analysis tools for post-processing CADD results.

Analysis of Next Generation DNA sequencing data

Existing and generated datasets for further analysis (e.g. database with genotype and phenotype data about patients with specific disorders), Workflows/pipelines for genomic data processing to address the identification of genetic mutations that cause rare diseases in families and of genetic variants that contribute to complex diseases such as autism and cancer, Easily-accessible workflow for non computing users to perform analysis, Workflows to identify the thermodynamic pattern of the genome influence fundamental processes of the cell such as transcription and RNA processing, Repositories of analysis tools for NGS datasets. Regarding the analysis of Next Generation DNA sequencing data, it will be ensured that all data follow the EU guidelines and regulations regarding anonymization and sharing of data:

  1. “Practice Guidelines for the Evaluation of Pathogenicity and the Reporting of Sequence Variants in Clinical Molecular Genetics”, Association for Clinical Genetic Science (2013)
  2. “Practice guidelines for Targeted Next Generation Sequencing Analysis and Interpretation”, Association for Clinical Genetic Science (2015)
  3. “Guidelines for diagnostic next-generation sequencing”, European Journal of Human Genetics (2016) 24, 2–5
 

Synchrotron data analysis

Existing and generated datasets for further analysis, Workflows for determining protein structures using infrared microspectroscopy and bioinformatics software, Workflows for processing large structural data segments, Repository of analysis tools for processing large structural data segments.

Image processing for biological applications

Workflow for image processing for biological applications, Databases of medically- relevant images

Computational simulation of DNA and RNA

existing and generated datasets for further analysis, Workflows for simulating a DNA or RNA with commonly-used codes (e.g. NAMD, GROMACS), repository of analysis tools for MD trajectories.

Available Modeling and Molecular Dynamics data

Description: This dataset contains Molecular Dynamics simulations trajectories of the dimer RAR-RXRa in the RXRa normal (wild-type) and mutated RXRa S427F form. The input and output files are in GROMACS format.

Use Licence: Free upon contacting the authors at This email address is being protected from spambots. You need JavaScript enabled to view it.
Contact: Zoe Cournia, Ioannis Galdadas
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Description: This dataset contains Molecular Dynamics simulations trajectories of the tetramer RXRa in the RXRa normal (wild-type) and three variations of the mutated RXRa S427F forms. The input and output files are in GROMACS format.

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Charge: Free upon contacting the authors at This email address is being protected from spambots. You need JavaScript enabled to view it.
Contact: Zoe Cournia, Ioannis Galdadas
e-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

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Charge: CC0 1.0 Universal
Contact: Bigovic, Miljan - Zecevic, Zarko

Description: Retinoic acid receptors (RARs) and Retinoid X nuclear receptors (RXRs) are ligand-dependent transcriptional modulators that execute their biological action through the generation of functional heterodimers. RXR acts as an obligate dimer partner in many signalling pathways, gene regulation by rexinoids depending on the ligated state of the specific heterodimeric partner. One of these dimers is formed with the retinoic acid receptor (RAR) or with , which is a type of nuclear receptor, which acts as a transcription factor. The dimer formation is protective in cancer. A single point mutation on RXRa, S427F, which is found in 5% of patients with bladder cancer, is located exactly at the dimerization interface; however its mechanism of action is unknown. To address the question of the effect of mutation on the dimerization of RXRa and RAR, we performed MD simulations to understand how the change of serine to phenyalanine at position 427 is suppressing the dimer function and is thus implicated in cancer.
This dataset contains Molecular Dynamics simulations trajectories of the normal (wild-type, WT) PI3Ka and the mutant H1047R PI3Ka. We provide two different datasets:\n1) MD simulations of only the catalytic subunit of PI3Ka (p110a), and without the regulatory subunit (p85a), in the WT and mutant H1047R forms (PI3Ka-with-p110a-without-p85a. These simulations are given in five independent replicate trajectories. The input and output files are in NAMD format. These simulations are described in Gkeka et al:\nhttp://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003895\n2) MD simulations of both the catalytic subunit of PI3Ka (p110a) and the regulatory subunit (p85a), in the WT and mutant H1047R forms (PI3Ka-with-p110a-with-p85a). One simulation set is performed in complex with the PI3Ka inhibitor, PIK-108, and another simulation set without an inhibitor (apo form). The apo forms are provided in both double and single precision for comparison. These simulations are described in Gkeka et al:\nhttp://pubs.acs.org/doi/abs/10.1021/jp506423e The input and output files are in GROMACS format.

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Charge: Free upon citing the publications

http://pubs.acs.org/doi/abs/10.1021/jp506423e

Contact: Zoe Cournia, Paraskevi Gkeka

Description: This dataset contains Molecular Dynamics simulations trajectories of the drug gemcitabine inside the pores of Metal-Organic FrameworksIRMOF-74-III and the functionalized OH-IRMOF-74-III. The input and output files are in GROMACS format.

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Charge: Free upon citing the publication http://pubs.acs.org/doi/abs/10.1021/jp506423
Contact: Zoe Cournia, Ioannis Galdadas

Description: "MD simulations of both the catalytic subunit of PI3Ka (p110a) and the regulatory subunit (p85a), in the WT and mutant H1047R forms (PI3Ka-with-p110a-with-p85a). One simulation set is performed in complex with the PI3Ka inhibitor, PIK-108, and another simulation set without an inhibitor (apo form). The apo forms are provided in both double and single precision for comparison. These simulations are described in Gkeka et al: http://pubs.acs.org/doi/abs/10.1021/jp506423e. The input and output files are in GROMACS format.".

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Charge: Free upon citing the publications

http://pubs.acs.org/doi/abs/10.1021/jp506423e

Contact: Zoe Cournia, Paraskevi Gkeka

Description: This dataset contains Molecular Dynamics simulations trajectories of the full length E545K oncogenic mutant of PI3Ka. These simulations are provided in four independent replicate trajectories (Run 1 and Replicate 1,2,3). We also provide an MD simulation of an artificial mutant where residues E545, K382, Q546, E542, R358 have been all mutated to alanine (ALA-mut.tar).

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Charge: Free upon contacting the authors
Contact: Hari Leontiadou, Ioannis Galdadas, Zoe Cournia

Description: This dataset contains Molecular Dynamics simulations trajectories of the full length Wild-Type (normal) PI3Ka. These simulations are provided in two independent replicate trajectories (Run 1 and Replicate 1).

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Charge: Free upon contacting the authors
Contact: Hari Leontiadou, Ioannis Galdadas, Zoe Cournia

Description: This dataset contains results of simulations concerning disordered proteins and single - stranded nucleic acids.

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Charge: Free
Contact: Yevgeni Mamasakhlisov 

Description: 3D molecular structures (proteins, polymers and surfactants).

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Charge: Free
Contact: Yevgeni Mamasakhlisov 

Available computer-aided design data

Description: Datasets from calculation of local mode frequencies (partial vibrational density of states) from classical or ab initio Molecular Dynamics Simulations.

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Use Licence: Free 
Contact: Marija Glavash Dodov
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Available Synchrotron data analysis datasets 

Description: The datasets contain the results of the SQP-IRS analysis.

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Use Licence: Free 
Contact: Gihan Kamel, Salman Matalgah
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Available datasets used for image processing for biological applications

Description: Datasets used as examples for running CCC code.

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Use Licence: Free 
Contact: Salman Matalgah
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Description: This databases contain information on genotype, and for some disorders also phenotype data, for more than 6000 patients with wide range of disease (from rare to common diseases).

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Charge: Free upon contacting the authors
Contact: Djordje Francuski 

Available computational simulation of DNA and RNA data

Description: Datasets on the thermodynamic pattern of the genome.

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Use Licence: Free 
Contact: Stoyno Stoynov 
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