• Computational quest for finding potential Ebola VP40 inhibitors: a molecular docking study = [pencarian pengiraan untuk mencari potensi perencat Ebola VP40: suatu kajian mengedok molekul]. (iium.edu.my)
  • They also conducted high-throughput laboratory screening experiments, structural studies, and molecular dynamics simulations to learn how these potential inhibitors and the enzyme interact. (bnl.gov)
  • In this research we designed isoindoel compounds as a novel L-HDH inhibitors and showed their efficiency by modeling studies and docking that at first the structure of desired compounds were build by using HYPERCHEM program. (ispub.com)
  • Our molecular simulation suggested each key amino acid, Tyr337 of AChE and Asn228 of BuChE, which were corresponded with potential inhibitors 1, and 3 and 4, respectively. (bvsalud.org)
  • Besides, we submitted the top three drugs to molecular dynamics simulations via Gromacs 2018.1. (nih.gov)
  • Clara for Drug Discovery includes a variety of tools and frameworks for molecular simulation, including GROMACS , NAMD , Tinker-HP , VMD , TorchANI , and DeePMD-Kit . (nvidia.com)
  • 2021 ) Triazole based isatin derivatives as potential inhibitor of key cancer promoting kinases- insight from electronic structure, docking and molecular dynamics simulations. (academictree.org)
  • AutoDock is a growing collection of methods for computational docking and virtual screening for use in structure-based drug discovery and exploration of the basic mechanisms of biomolecular structure. (nvidia.com)
  • Machine learning for yield prediction for chemical reactions using in situ sensors JOURNAL OF MOLECULAR GRAPHICS & MODELLING. (nottingham.ac.uk)
  • Finally, combined quantum mechanical/molecular mechanical (QM/MM) modelling of the IdmH reaction shows that the active site of the enzyme provides an appropriate environment to promote indane-ring formation, supporting the assignment of IdmH as the key Diels-Alderase catalysing the final step in the biosynthesis of indanomycin through a similar mechanism to other recently characterized Diels-Alderases involved in polyketide-tailoring reactions. (iucr.org)
  • A Computational Investigation on Chitosan Derivatives using Pharmacophore- based Screening, Molecular Docking, and Molecular Dynamics Simulations against Kaposi Sarcoma. (bvsalud.org)
  • J. Xu, J. Z. H. Zhang and Y. Xiang, "Molecular Dynamics Simulation and Computational Two-Dimensional Infrared Spectroscopic Study of Model Amyloid β-Peptide Oligomers," The Journal of Physical Chemistry A, Vol. 117, No. 29, 2013, pp. 6373-6379. (scirp.org)
  • Summit's computational horsepower is the engine for driving more reliable, predictable flow models for multi-scale, multi-physics simulation. (nvidia.com)
  • The main focus of our research is the development and optimization for High-Performing-Computing (HPC) of computational methodology for the structural and energetic characterization of protein interactions at molecular level. (bsc.es)
  • In the present study, through extensive computational docking and multi-ns molecular dynamics (MD) simulation, we evaluated if cyclotides can stably bind to Aβ molecules and/or destabilize the Aβ fibril by preventing conformational changes from α-helical to β-sheet rich structures. (ncbs.res.in)
  • S. Dhar, D. K. Rana, A. Pal and S. C. Bhattacharya, "Photobehavior and Docking Simulations of Drug within Macromolecules: Binding of an Antioxidative Isoquino- lindione to a Serine Protease and Albumin Proteins," Journal of Photochemistry and Photobiology B: Biology, Vol. 129, 2013, pp. 69-77. (scirp.org)
  • D. Ray, B. K. Paul and N. Guchhait, "Differential Binding Modes of Anti-Cancer, Anti-HIV Drugs Belonging to Isatin Family with a Model Transport Protein: A Joint Refinement from Spectroscopic and Molecular Modeling Approaches," Journal of Photochemistry and Photobiology B: Biology, Vol. 127, 2013, pp. 18-27. (scirp.org)
  • From large language models (LLMs) that generate de novo proteins, small molecules, and the 3D structure of a protein to molecular dynamic simulations, novel deep learning techniques are changing the way that scientists explore the ever-expanding chemical and biological research space. (nvidia.com)
  • We have also made available our software through different web servers, such as pyDockWeb for protein-protein docking, pyDockSAXS for the structural prediction of protein complexes using Small-Angle X-ray Scattering (SAXS) data in collaboration with Pau Bernadó (CBS, Montpellier), or OPRA for the identification of RNA-binding residues in proteins. (bsc.es)
  • More efficient identification of correct docking poses, especially in difficult cases such as weak interactions, multi-protein complexes or membrane proteins. (bsc.es)
  • The stability of interacting residues of proteins with compounds was identified via molecular dynamics and free binding energy calculations using Amber 12. (ui.ac.id)
  • Molecular dynamics simulations offer a fantastic opportunity to see how proteins work. (lu.se)
  • The implemented routines analyze the protein environment of water molecules in molecular dynamics (MD) simulations and can differentiate between hydrogen bonded waters as well as waters in a protein environment of hydrophobic, charged, or aromatic atom groups. (acs.org)
  • PyRod adds a new perspective to structure-based screening campaigns by providing easy-to-interpret dMIFs and purely protein-based pharmacophores that are solely based on tracing water molecules in MD simulations. (acs.org)
  • Another aspect of Hirst's research focuses on the study of protein-ligand interactions, using techniques including QSAR, machine learning, neural networks, docking, molecular dynamics (MD) simulations and quantum chemistry. (nottingham.ac.uk)
  • This includes gene, protein and metabolic networks, cellular architecture and intracellular dynamics, cell communication and motility, cell division and differentiation, tissue formation and organogenesis, tissue and organ functions, changes in population characteristics as a consequence of interaction of organisms with their physical environment, with individuals of their own species, and with organisms of other species. (nih.gov)
  • GPU-powered molecular dynamics frameworks can simulate the fundamental mechanisms of cells and calculate how strongly a candidate drug will bind to its intended protein target. (nvidia.com)
  • S. Jana, S. Dalapati, S. Ghosh and N. Guchhait, "Binding Interaction between Plasma Protein Bovine Serum Albumin and Flexible Charge Transfer Fluorophore: A Spectroscopic Study in Combination with Molecular Docking and Molecular Dynamics Simulation," Journal of Photochemistry and Photobiology A: Chemistry, Vol. 231, No. 1, 2012, pp. 19-27. (scirp.org)
  • Among others, we have developed software for prediction of protein-protein complex structure by docking simulations, identification of binding sites on protein surfaces, or prediction of hot-spot residues from energy calculations. (bsc.es)
  • The treatment of protein flexibility is currently a major bottleneck in protein docking. (bsc.es)
  • We are continuously validating our docking methods in CAPRI , a world-wide community experiment that aims to evaluate the current state of protein-protein docking prediction. (bsc.es)
  • Molecular docking was performed to evaluate the binding affinity of 97 phenolic compounds (phenolics) with the SARS-CoV-2 S-protein receptor-binding domain (RBD). (elis.sk)
  • Molecular dynamics (MD) simulation was carried out to assess the stability of interactions between top-ranked compounds and S-protein RBD. (elis.sk)
  • One of the conserved hydrophobic interface residues, Tyr10 was mutated to Ala and the impact of this virtual mutation was estimated by additional MD simulations for the wild-type (WT) and mutant protein-peptide complexes. (ncbs.res.in)
  • In this study, emodin derivatives were conducted as an inhibitor candidate of capsid assembly by disruption formation dimer-dimer HBV core protein using molecular docking and dynamic simulation. (ui.ac.id)
  • Methods: Structure-based virtual docking approach was used to design of benzoylated emodin derivatives into HBV core protein as receptor using Molegro Virtual Docker 6.0 program. (ui.ac.id)
  • By following the movement of every single atom under the influence of the forces from all other atoms, we get an extremely detailed picture of protein dynamics. (lu.se)
  • Development of new or improved laboratory/experimental techniques, instruments, or supporting software that measure the location and dynamics of molecules in situ, and organelles, cells, or tissues on the nanometer and micrometer length scales. (nih.gov)
  • The team used computer-based molecular docking studies to identify molecules that could bind to certain targets on the virus's main protease (Mpro)-an enzyme the virus uses to make copies of itself. (bnl.gov)
  • International journal of molecular sciences 2023 0 0. (cdc.gov)
  • Human molecular genetics 2023 0 0. (cdc.gov)
  • Nearly, 100 ns MD simulation indicated the stability of the designed compounds at 100 ns, while molecular mechanics-Poisson Boltzmann surface area calculation showed that the designed compound had a higher affinity than that of the parent compound. (japsonline.com)
  • Highest occupied molecular orbital and lowest unoccupied molecular orbital were analysed to determine the lead compounds' biological and pharmacological efficacy . (bvsalud.org)
  • Molecular Docking of Polyphenol Compounds from Anacardium occidentalewith Alpha-Glucosidase and Dipeptidyl-Peptidase-4 Enzymes. (iium.edu.my)
  • The chemical structures of isoindoles (table.1) were constructed using Hyperchem software (version 7, Hypercube Inc.) .Semi-empirical molecular orbital calculations ( PM3) of the structure were performed using the Hyperchem program and the among all energy minima conformers, the global minimum of compounds were consider in docking calculations. (ispub.com)
  • Molecular Docking and Dynamics Simulation of Natural Phenolic Compounds with GSK-3β: A Putative Target to Combat Mortality in Patients with COVID-19. (cdc.gov)
  • The gathered information is further processed to generate dynamic molecular interaction fields (dMIFs) for visualization and pharmacophoric features for virtual screening. (acs.org)
  • The results revealed that the top hits responded to all of the pharmacological druglikening criteria and had the best interaction residues, fitness scores, and docking scores. (bvsalud.org)
  • Through molecular dynamics we have analysed the stability of the ISCA1-cryptochrome complex and characterized the interaction at the binding sites between individual cryptochrome and ISCA1. (nature.com)
  • M. Memarpoor-Yazdi and H. Mahaki, "Probing the Interaction of Human Serum Albumin with Vitamin B2 (Riboflavin) and l-Arginine (l-Arg) Using Multi-Spectroscopic, Molecular Modeling and Zeta Potential Techniques," Journal of Luminescence, Vol. 136, 2013, pp. 150-159. (scirp.org)
  • We try to solve both these problems by developing new simulation algorithms and interaction models, as well as adapting existing methods to new systems. (lu.se)
  • The aim of this research was to compare three modeling approaches (Docking, molecular dynamics (MD), and quantum mechanics (QM)) for cyclodextrin/drug complexation. (hindawi.com)
  • Molecule modeling method is able to investigate the structure, dynamics, and energetics of cyclodextrin systems. (hindawi.com)
  • Homology modeling and docking studies of δ19-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. (iium.edu.my)
  • Several weather and ocean modeling applications such as the Weather Research and Forecasting (WRF) model and tsunami simulations are achieving tremendous speedups, of more than 5X, that help save time and improve accuracy. (nvidia.com)
  • Using the built model, a novel compound was proposed, and molecular docking and molecular dynamics simulation were then used to check the conformational stability of the newly proposed compound in the binding site of EGFR. (japsonline.com)
  • The use of unbound conformational ensembles prior to docking dramatically improve the predictive results in medium-flexible cases. (bsc.es)
  • Inclusion of conformational flexibility by using conformational ensembles, interface refinement, and coarse-grained flexible docking. (bsc.es)
  • Effects of a plant cyclotide on conformational dynamics and destabilization of β-amyloid fibrils through molecular dynamics simulations. (ncbs.res.in)
  • Docking results from AutoDock Vina program showed that the scoring of complexation capability between ibuprofen and cyclodextrins is alpha ( α ), gamma ( γ ), beta ( β ), and HP-beta-cyclodextrins, which indicated similar ranking with the results from phase, solubility diagram experiments. (hindawi.com)
  • Then Docking calculations were carried out using AutoDock program (Ver4) program. (ispub.com)
  • Docking studies were carried out by using the program AUTODOCK 4. (ispub.com)
  • Molecular docking and MD simulations were performed utilizing the AutoDock and Discovery Studio Client version, respectively. (elis.sk)
  • probes, molecular reporters and fluorescent indicators for structural or functional imaging or microscopy/nanoscopy. (nih.gov)
  • Unveiling the molecular mechanisms underpinning biorecognition of early-glycated human serum albumin and receptor for superior glycation finish merchandise. (atto-gentaur.com)
  • Exploration of the Shared Molecular Mechanisms between COVID-19 and Neurodegenerative Diseases through Bioinformatic Analysis. (cdc.gov)
  • We are using the capabilities of MareNostrum to develop new algorithms based on molecular dynamics approaches. (bsc.es)
  • From weather prediction and materials science to wind tunnel simulation and genomics, NVIDIA GPU-accelerated computing is at the heart of HPC's most promising areas of discovery. (nvidia.com)
  • We carried out a series of bioinformatics studies with the phytoconstituents of Amaranthus tricolor to elicit their possible molecular functions in cognitive disorders including Alzheimer's disease. (ijpsonline.com)
  • Docking studies were carried out with AutoDock4.2v. Molecular dynamics analyses were performed using Schrodinger Desmond 6.1v software for a 50 ns production run. (ijpsonline.com)
  • Molecular docking and molecular dynamics simulations studies on β-glucosidase and xylanase Trichoderma asperellum to predict degradation order of cellulosic components in oil palm leaves for nanocellulose preparation. (iium.edu.my)
  • A docked model of a Ube2S-donor ubiquitin complex was generated previously, based on chemical shift mapping by NMR, and predicted contacts were validated in functional studies. (rcsb.org)
  • The scope of the systems covered ranges from cellular to tissue, organ, systems studies, and up to populational dynamics. (nih.gov)
  • Additionally, molecular docking studies indicated compound 10 had the ability to form six hydrogen bonds at sEH active site, resulting binding energy as low as -9.58â Kcal/mol. (bvsalud.org)
  • The aim was to assess the effectiveness of available FDA approved drugs which can construct a covalent bond with Cys145 inside binding site SARS-CoV-2 main protease by using covalent docking screening. (nih.gov)
  • The 50 ns molecular dynamics simulation was conducted for saquinavir, ritonavir and remdesivir to evaluate the stability of these drugs inside the binding pocket of SARS-CoV-2 main protease. (nih.gov)
  • Machine-learned potentials, which show promise for quantum mechanical-level accuracy, energies, and forces, are fundamentally changing molecular simulation. (nvidia.com)
  • The importance of hydrogen bonding and ringâ ring interactions is explored along with an examination of the major docking arrangements. (sharcnet.ca)
  • Kaempferol exhibited the highest binding affinity with acetylcholinesterase, monoamino oxidase A and monoamino oxidase B. Molecular dynamics simulation demonstrated stable intermolecular interactions between kaempferol and acetylcholinesterase. (ijpsonline.com)
  • Additional computer-based simulations provided details about how those interactions alter the enzyme. (bnl.gov)
  • MD simulation indicated that ibuprofen could form the stable complexes with β -, γ -, and HP- β -cyclodextrins, but not for alpha cyclodextrin. (hindawi.com)
  • The crystallographic interface is more hydrophobic than the earlier model and is stable in molecular dynamics (MD) simulations. (rcsb.org)
  • Binding free energy from three simulation methods was calculated as an important parameter to compare with the experimental results. (hindawi.com)
  • The results of our docking methods have been overall highly encouraging (within top 5 groups out of more than 60 participants in both the 5th and 6th CAPRI editions). (bsc.es)
  • New efficient docking methods for HPC implementation. (bsc.es)
  • Our study was limited to computer simulations and calls for wet lab validation of the predicted molecular functions. (ijpsonline.com)
  • The top hits were examined using molecular docking , absorption , distribution, metabolism and excretion. (bvsalud.org)
  • A detailed MD simulation analyses revealed that cyclotides form hydrogen bonds with the toxic amyloid assemblies thereby weakening the inter-strand hydrogen bonds between the Aβ peptide. (ncbs.res.in)
  • Finally Docking calculations were carried out using Auto-Dock program. (ispub.com)
  • In-depth analysis of F389V through Molecular Docking and Dynamics Simulation revealed a decline in affinity for its native agonist dopamine and an increase in affinity for the antipsychotic drug risperidone. (biorxiv.org)
  • Shared molecular signatures between coronavirus infection and neurodegenerative diseases provide targets for broad-spectrum drug development. (cdc.gov)
  • It is now well-established that from early lesion to vulnerable plaque formation, numerous cellular and molecular inflammatory components participate in the disease process. (researchgate.net)
  • Gene ontology functional enrichment analysis revealed twenty eight biological processes and 10 molecular functions associated with cognitive impairment. (ijpsonline.com)
  • Remarkably, the docked Ube2S-donor complex converges readily to the configuration seen in the crystal structure in 3 out of 8 MD trajectories. (rcsb.org)
  • This truncated variant allows consistent and easy crystallization, but importantly the structure was used as a search model in molecular replacement, allowing the full-length IdmH structure to be determined to 2.7 Å resolution. (iucr.org)
  • However, cyclodextrins are poor across most of the biological membranes due to their high molecular weight and inherent hydrophilicity [ 2 ]. (hindawi.com)
  • Binding free energies from the MD simulation for β -, γ -, and HP- β -cyclodextrins were −3.67, −0.67, and −3.87 kcal/mol, individually. (hindawi.com)
  • Molecular Dynamic (MD) and Monte Carlo (MC) simulations were performed on the three polymers complexed with Pb(II). (biomedcentral.com)