Results 311 to 320 of about 109,425 (326)

Fully Flexible Docking via Reaction-Coordinate-Independent Molecular Dynamics Simulations

Journal of Chemical Information and Modeling, 2018
Predicting the geometry of protein-ligand binding complexes is of primary importance for structure-based drug discovery. Molecular dynamics (MD) is emerging as a reliable computational tool for use in conjunction with, or an alternative to, docking methods. However, simulating the protein-ligand binding process often requires very expensive simulations.
BERTAZZO, MARTINA, BERNETTI, MATTIA, Recanatini, Maurizio, Masetti, Matteo, Cavalli, Andrea   +4 more
openaire   +2 more sources

Molecular docking and molecular dynamics simulation studies on PLCE1 encoded protein

Journal of Molecular Structure, 2019
Abstract Phospholipase C epsilon gene (PLCE1) is encoded the 1-phosphatidylinositol 4,5- bisphosphate phosphodiesterase ɛ-1 protein. This protein is characterized by the fetal onset of enormous proteinuria following by severe steroid resistance nephrotic syndrome (SRNS). The mutation position is located on the PIPLC_X domain of PLCE1 encoded protein.
Satya Narayan Sahu, Subrat Kumar Pattanayak   +1 more
openaire   +1 more source

Molecular docking, 3D-QASR and molecular dynamics simulations of benzimidazole Pin1 inhibitors

Physical Chemistry Chemical Physics
Molecular docking, 3D-QSAR, dynamics simulations, free energy and decomposition calculation between Pin1 protein and benzimidazole Pin1 inhibitors.
Min Liu, Bingli Wang, Huan Liu, Haolun Xia, Lina Ding   +4 more
openaire   +2 more sources

Molecular docking and molecular dynamics simulation decoding molecular mechanism of EDCs binding to hERRγ

Journal of Molecular Modeling
Human estrogen-related receptor γ (hERRγ) is a key protein involved in various endocrines and metabolic signaling. Numerous environmental endocrine-disrupting chemicals (EDCs) can impact related physiological activities through receptor signaling pathways.
Ying, Sun, Lin, Chen, Bing, Zhao, Ruige, Wang   +3 more
openaire   +2 more sources

Simulation of Carbohydrates, from Molecular Docking to Dynamics in Water

2012
Modeling of carbohydrates is particularly challenging because of the variety of structures resulting for the high number of monosaccharides and possible linkages and also because of their intrinsic flexibility. The development of carbohydrate parameters for molecular modeling is still an active field.
Nicolas, Sapay, Alessandra, Nurisso, Anne, Imberty   +2 more
openaire   +2 more sources

Reranking Docking Poses Using Molecular Simulations and Approximate Free Energy Methods

Journal of Chemical Information and Modeling, 2014
Fast and accurate identification of active compounds is essential for effective use of virtual screening workflows. Here, we have compared the ligand-ranking efficiency of the linear interaction energy (LIE) method against standard docking approaches. Using a trypsin set of 1549 compounds, we performed 12,250 molecular dynamics simulations.
Lauro, G., Ferruz, N., Fulle, S., Harvey, M. J., Finn, P. W., De Fabritiis, G.   +5 more
openaire   +4 more sources

Molecular Dynamics Simulation and Docking of MUC1 O-Glycopeptide

Advances in computer performance and computational simulations allow increasing sophistication in applications in biological systems. Molecular dynamics (MD) simulations are especially suitable for studying conformation, dynamics, and interaction of flexible biomolecules such as free glycans and glycopeptides.
Ryoka, Kokubu, Shiho, Ohno, Noriyoshi, Manabe, Yoshiki, Yamaguchi   +3 more
openaire   +2 more sources

Molecular docking and molecular dynamics simulation

2022
Sakshi Singh, Qanita Bani Baker, Dev Bukhsh Singh   +2 more
openaire   +1 more source

Automated Ligand Design in Simulated Molecular Docking

The 2022 Conference on Artificial Life, 2022
Rob Maccallum, Geoff Nitschke
openaire   +1 more source

AI-ENHANCED MOLECULAR DOCKING AND DRUG BINDING SIMULATIONS

In recent years, the intersection of artificial intelligence (AI) and chemistry has sparked a profound transformation in molecular science. As we stand on the brink of a new era in scientific discovery, the application of AI technologies promises to revolutionize the way we understand, analyze, and manipulate chemical systems.
Khan, Arbaz, Kumar, Samit
openaire   +1 more source