Contributors: Yevgen Yurenko, Martin Lepšík, Juraj Dobiaš
... The dataset contains molecular dynamics trajectories of 300ns simulation of three complexes of Helidye1, a novel cationic helicene-like probe for DNA detection, with double-stranded DNA. In addition to trajectories, we add parameter files (mol2 and frc) for HeliDye1 containing atomic charges and parameter for dihedral and improper torsion angles.
Induction of Rare Conformation of Oligosaccharide by Binding to Calcium-dependent Bacterial Lectin: X-ray Crystallography and Modelling Study
Contributors: Martin Lepsik, Anne Imberty
... Parameters, inputs and trajectories for 600 ns molecular dynamics of Pseudomonas aeruginosa lectin LecB in complex with Lewis x tetrasaccharide using the most promising Setup4 (see the publication).
Contributors: Guitang Wang
... Mitohondrial gene orders of 32 Neodermata representatives used for CREx, TreeREx and MLGO analyses in the article: "Homoplasy or plesiomorphy? Reconstruction of the evolutionary history of mitochondrial gene order rearrangements in the subphylum Neodermata"
Data for: Structural modifications of 2,3-indolobetulinic acid: design and synthesis of highly potent α-glucosidase inhibitors
Contributors: Elmira Khusnutdinova, Thi Tu Anh Le, Tra Nguyen Thanh, Anastasiya V. Petrova, Denis Babkov, Oxana Kazakova, Ha Nguyen Thi Thu, Cham Ba Thi
... A series of nineteen nitrogen-containing lupane triterpenoids was obtained by modification of C2, C3, C20 and C28 positions of betulonic acid and their α-glucosidase inhibiting activity was investigated. Being a leader compound from our previous study, 2,3-indolo-betulinic acid was used as the main template for different modifications at C-(28)-carboxyl group to obtain cyano-, methylcyanoethoxy-, propargyloxy- and carboxamide derivatives. 20-Oxo- and 29-hydroxy-20-oxo-30-nor-analogues of 2,3-indolo-betulinic acid were synthesized by ozonolysis of betulonic acid followed by Fischer indolization reaction. To compare the influence of the fused indole or the seven membered A-ring on the inhibitory activity, lupane A-azepanones with different substituents at C28 were synthesized. The structure-activity relationships revealed that the enzyme inhibition activity dramatically increased (up to 4730 times) when the carboxylic group of 2,3-indolo-betulinic acid was сonverted to the corresponding amide. Thus, the IC50 values for glycine amide and L-phenylalanine amides were 0.04 and 0.05 μM, respectively. This study also revealed that 2,3-indolo-platanic acid is 4.5 times more active than the parent triterpenoid with IC50 of 0.4 μM. Molecular modeling suggested that improved potency is due to additional polar interactions formed between C28 side chain and a sub-pocket of the α-glucosidase allosteric site.
Data for: Multi-gene global phylogeography of the Gypsy Moth, reveals misaligned subspecies concepts and a cryptic lineage
Contributors: Reza Zahiri, B. Christian Schmidt, Michal Rindos, Alexander Schintlmeister, Roman V. Yakovlev
... Various datasets used in this study are uploaded here.
Contributors: luz america chi uluac, M. Cristina Vargas González
... In silico design of peptides to target resistin algorithm Binding free energy (peptide-protein) script We have been able to design a great set of peptides with high scoring binding energy to resistin. Further, two peptides were chosen, to perform a more rigorous calculation of binding free energy based on the Alchemical Absolute Binding Free Energy method. We were able to establish a methodological route for the development of strong candidates for the design of ligands to resistin.
Contributors: Yong D. Dai, Hong Yu, Zhu L. Yang, Yuan B. Wang, Xuan X. Mo, Da R. Yang, Yao Wang
... The mitochondrial cytochrome oxidase I gene (cox1) were sequenced and analyzed among 710 samples representing 88 geographic locations. 205 haplotypes of cox1 were identified. Four clades with 12 subclades were identified. Dating analyses from 3 calibrations supported that the divergence of the 4 clades happened in the Oligocene -Miocene (30.54-13.66 million years ago)
Contributors: Jiaming Qi
... Whole-genome sequencing of Bacillus subtilis BS-6. Leading Bio-agricultural Co., Ltd.
Contributors: Enade Perdana Istyastono
... A model of full human matrix metalloproteinase 9 with ligands from PDB:4H3X and PDB:1ITV from homology modeling studies using YASARA Structure.
Transcriptomic responses of the clam Meretrix meretrix to the organophosphorus pesticide (dimethoate)
Contributors: Jun Cao
... Transcriptomic responses of the clam Meretrix meretrix to the organophosphorus pesticide (dimethoate)