VI-SEEM Life Sciences
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The VI-SEEM Life Sciences Community repository
2016 The VI-SEEM Consortium Life Sciences Community
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D3R
D3R datasets -
Misc
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PSOMI
Collection related to the PSOMI Application -
Training Material
The Life Sciences Training Material -
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This sub-section contains workflows of the VI-SEEM Life Sciences community
Recent Submissions
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Sequence Prediction Algorithms vs. Infrared Spectroscopy for Proteins Secondary Structure Optimization
(2018-09-28)More than 80% of the known protein structures are determined using the Macromolecular Crystallography (MX) technique that is feasible in only Synchrotron light facilities. Two difficulties may arise in this case: (1) the ... -
Thermodynamic patterns of eukaryotic genes
(2018)As it reads the information encoded throughout the genome, RNA polymerase II can travel along the DNA template for thousands of nucleotides. In the process, it encounters the physical forces of DNA/DNA and RNA/DNA pairing ... -
CCC Cancer Cells Classification
(2017-06-15) -
Dataset from the study “SEMIEMPIRICAL ATOM-CENTERED DENSITY MATRIX PROPAGATION APPROACH TO TEMPERATURE-DEPENDENT VIBRATIONAL SPECTROSCOPY OF IRINOTECAN”
(West University of Timișoara, 2018-05-17)This dataset contains the complete molecular dynamics (MD) trajectories of free irinotecan molecule at several temperatures. MD study of irinotecan molecule was carried out with the atom-centered density matrix propagation ... -
Computer-aided drug design to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2
Computer-aided drug design has become an integral part of drug discovery and development efforts in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead ... -
Calculation of Local Mode Frequencies (Partial Vibrational Density of States) from Classical or AB Initio Molecular Dynamics Simulations
(West University of Timișoara, 2017)Development of analytic derivatives techniques in computational quantum chemistry has paved the way towards practically routine algorithms for computation of vibrational spectroscopic properties of even large molecular ... -
Principles of Computer-Aided Drug Design
(BRFAA, 2016-10-21)Principles of Computer-Aided Drug Design -
Molecular Dynamics simulations of lysozyme in water
(BRFAA, 2015-05-02)The main objective of this practical is to provide an overview of classical Molecu- lar Dynamics (MD) simulations and Normal Mode Analysis (NMA) by examining the protein Lysozyme within the framework of the NAMD program. -
Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations
The kinase PI3Ka is involved in fundamental cellular processes such as cell proliferation and differentiation and is frequently mutated in human malignancies. One of the most common mutations is E545K, which ... -
Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant
The PIK3CA gene is one of the most frequently mutated oncogenes in human cancers. It encodes p110a the catalytic subunit of phosphatidylinositol 3-kinase alpha (PI3Ka which activates signaling cascades leading to cell ... -
Exploring a Non-ATP Pocket for Potential Allosteric Modulation of PI3Kα
Allosteric modulators offer a novel approach for kinase inhibition because they target less conserved binding sites compared to the active site; thus, higher selectivity may be obtained. PIK-108, a known pan phosphoinositide ... -
Investigating the effect of RXRa S427F mutant on RXRa tetramers
Retinoid X nuclear receptors (RXRs) are ligand-dependent transcriptional modulators that execute their biological action through the generation of functional heterodimers. Biochemical data indicate that, in the absence of ... -
Metal-Organic Frameworks as drug delivery systems: The case of IRMOF-74-III and gemcitabine studied by MD simulations
(BRFAA, 2017-04-27)A multiscale computational study is reported that investigates the microscopic behavior of the anti-cancer drug gemcitabine (GEM) stored in metal organic frameworks IRMOF-74-III and the functionalized OH-IRMOF-74-III. ... -
PSOMI - VERSION 1
(2016-12)
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