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Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites.
- Published in:
- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-51511-6
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- Article
Effects of Indocyanine Green (ICG) Imaging-Assisted Cholecystectomy on Intraoperative and Postoperative Complications: A meta-Analysis.
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- Surgical Innovation, 2024, v. 31, n. 4, p. 362, doi. 10.1177/15533506241246335
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- Article
Strategic advancement of E3 ubiquitin ligase in the management of hepatocellular carcinoma.
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- Medical Oncology, 2024, v. 41, n. 7, p. 1, doi. 10.1007/s12032-024-02411-8
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- Article
Versatile Self-Assembly of Triblock Peptides into Stable Collagen Mimetic Heterotrimers.
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- International Journal of Molecular Sciences, 2024, v. 25, n. 12, p. 6550, doi. 10.3390/ijms25126550
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- Article
Study of andrographolide bioactivity against Pseudomonas aeruginosa based on computational methodology and biochemical analysis.
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- Frontiers in Chemistry, 2024, p. 1, doi. 10.3389/fchem.2024.1388545
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- Article
Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence.
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- Nucleic Acids Research, 2024, v. 52, n. 6, p. 3433, doi. 10.1093/nar/gkae171
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- Article
TRIM5 as a promising diagnostic biomarker of hepatocellular carcinoma: integrated analysis and experimental validation.
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- Functional & Integrative Genomics, 2024, v. 24, n. 2, p. 1, doi. 10.1007/s10142-024-01339-6
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- Article
Revealing the Interaction Mechanism between Mycobacterium tuberculosis GyrB and Novobiocin, SPR719 through Binding Thermodynamics and Dissociation Kinetics Analysis.
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- International Journal of Molecular Sciences, 2024, v. 25, n. 7, p. 3764, doi. 10.3390/ijms25073764
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- Article
Computational methods for unlocking the secrets of potassium channels: Structure, mechanism, and drug design.
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- WIREs: Computational Molecular Science, 2024, v. 14, n. 1, p. 1, doi. 10.1002/wcms.1704
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- Article
Discovery of novel and potent InhA direct inhibitors by ensemble docking-based virtual screening and biological assays.
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- Journal of Computer-Aided Molecular Design, 2023, v. 37, n. 12, p. 695, doi. 10.1007/s10822-023-00530-4
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- Article
Causal associations between gut microbiota and primary biliary cholangitis: a bidirectional two-sample Mendelian randomization study.
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- Frontiers in Microbiology, 2023, p. 01, doi. 10.3389/fmicb.2023.1273024
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- Article
Application of computational approaches in biomembranes: From structure to function.
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- WIREs: Computational Molecular Science, 2023, v. 13, n. 6, p. 1, doi. 10.1002/wcms.1679
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- Article
Biological Evaluation of 8-Methoxy-2,5-dimethyl-5H-indolo[2,3-b] Quinoline as a Potential Antitumor Agent via PI3K/AKT/mTOR Signaling.
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- International Journal of Molecular Sciences, 2023, v. 24, n. 20, p. 15142, doi. 10.3390/ijms242015142
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- Article
MpbPPI: a multi-task pre-training-based equivariant approach for the prediction of the effect of amino acid mutations on protein–protein interactions.
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- Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad310
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- Article
Improving drug-target affinity prediction via feature fusion and knowledge distillation.
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- Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad145
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- Article
The α-Synuclein Monomer May Have Different Misfolding Mechanisms in the Induction of α-Synuclein Fibrils with Different Polymorphs.
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- Biomolecules (2218-273X), 2023, v. 13, n. 4, p. 682, doi. 10.3390/biom13040682
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- Article
Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning?
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad008
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- Article
Identification of CBPA as a New Inhibitor of PD-1/PD-L1 Interaction.
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- International Journal of Molecular Sciences, 2023, v. 24, n. 4, p. 3971, doi. 10.3390/ijms24043971
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- Article
Predicting molecular properties based on the interpretable graph neural network with multistep focus mechanism.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac534
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- Article
Design, Synthesis and Biological Evaluation of Neocryptolepine Derivatives as Potential Anti-Gastric Cancer Agents.
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- International Journal of Molecular Sciences, 2022, v. 23, n. 19, p. 11924, doi. 10.3390/ijms231911924
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- Article
fastDRH: a webserver to predict and analyze protein–ligand complexes based on molecular docking and MM/PB(GB)SA computation.
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- Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac201
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- Article
Binding Thermodynamics and Dissociation Kinetics Analysis Uncover the Key Structural Motifs of Phenoxyphenol Derivatives as the Direct InhA Inhibitors and the Hotspot Residues of InhA.
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- International Journal of Molecular Sciences, 2022, v. 23, n. 17, p. 10102, doi. 10.3390/ijms231710102
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- Article
A Novel Isaindigotone Derivative Displays Better Anti-Proliferation Activities and Induces Apoptosis in Gastric Cancer Cells.
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- International Journal of Molecular Sciences, 2022, v. 23, n. 14, p. 8028, doi. 10.3390/ijms23148028
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- Article
Thermodynamic integration combined with molecular dynamic simulations to explore the cross‐resistance mechanism of isoniazid and ethionamide.
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- Proteins, 2022, v. 90, n. 5, p. 1142, doi. 10.1002/prot.26295
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- Article
Application advances of deep learning methods for de novo drug design and molecular dynamics simulation.
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- WIREs: Computational Molecular Science, 2022, v. 12, n. 3, p. 1, doi. 10.1002/wcms.1581
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- Article
Discovery of Novel HPK1 Inhibitors Through Structure-Based Virtual Screening.
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- Frontiers in Pharmacology, 2022, v. 13, p. 1, doi. 10.3389/fphar.2022.850855
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- Article
Deciphering the Effect of Lysine Acetylation on the Misfolding and Aggregation of Human Tau Fragment 171 IPAKTPPAPK 180 Using Molecular Dynamic Simulation and the Markov State Model.
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- International Journal of Molecular Sciences, 2022, v. 23, n. 5, p. 2399, doi. 10.3390/ijms23052399
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- Article
Molecular dynamics simulations reveal the disruption mechanism of a 2,4‐thiazolidinedione derivative C30 against tau hexapeptide (PHF6) oligomer.
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- Proteins, 2022, v. 90, n. 1, p. 142, doi. 10.1002/prot.26196
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- Article
TrimNet: learning molecular representation from triplet messages for biomedicine.
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- Briefings in Bioinformatics, 2021, v. 22, n. 4, p. 1, doi. 10.1093/bib/bbaa266
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- Article
MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm.
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- Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa161
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- Article
Discovery of novel IDO1 inhibitors via structure-based virtual screening and biological assays.
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- Journal of Computer-Aided Molecular Design, 2021, v. 35, n. 5, p. 679, doi. 10.1007/s10822-021-00386-6
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- Article
Molecular Dynamics Simulations Study on the Resistant Mechanism of Insects to Imidacloprid due to Y151-S and R81T Mutations in nAChRs.
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- Molecular Informatics, 2019, v. 38, n. 8/9, p. 1, doi. 10.1002/minf.201800125
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- Article
The molecular mechanism of pH‐regulating C3d‐CR2 interactions: Insights from molecular dynamics simulation.
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- Chemical Biology & Drug Design, 2019, v. 93, n. 4, p. 628, doi. 10.1111/cbdd.13460
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- Article
Computational studies on horseshoe shape pocket of human orexin receptor type 2 and boat conformation of suvorexant by molecular dynamics simulations.
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- Chemical Biology & Drug Design, 2018, v. 92, n. 1, p. 1221, doi. 10.1111/cbdd.13181
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- Article
The molecular mechanism of two coreceptor binding site antibodies X5 and 17b neutralizing HIV‐1: Insights from molecular dynamics simulation.
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- Chemical Biology & Drug Design, 2018, v. 92, n. 1, p. 1357, doi. 10.1111/cbdd.13201
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- Article
Influence of EGCG on α-synuclein (αS) aggregation and identification of their possible binding mode: A computational study using molecular dynamics simulation.
- Published in:
- Chemical Biology & Drug Design, 2018, v. 91, n. 1, p. 162, doi. 10.1111/cbdd.13067
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- Article
Molecular dynamics simulation, binding free energy calculation and unbinding pathway analysis on selectivity difference between FKBP51 and FKBP52: Insight into the molecular mechanism of isoform selectivity.
- Published in:
- Proteins, 2018, v. 86, n. 1, p. 43, doi. 10.1002/prot.25401
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- Article
The glycan-mediated mechanism on the interactions of gp120 with CD4 and antibody: Insights from molecular dynamics simulation.
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- Chemical Biology & Drug Design, 2017, v. 90, n. 6, p. 1237, doi. 10.1111/cbdd.13045
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- Article
Discovery of small molecules binding to the normal conformation of prion by combining virtual screening and multiple biological activity evaluation methods.
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- Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 12, p. 1053, doi. 10.1007/s10822-017-0086-6
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- Article
Molecular Dynamics Studies on the Enzalutamide Resistance Mechanisms Induced by Androgen Receptor Mutations.
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- Journal of Cellular Biochemistry, 2017, v. 118, n. 9, p. 2792, doi. 10.1002/jcb.25928
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- Article
Molecular dynamics simulation on the inhibition mechanism of peptide-based inhibitor of islet amyloid polypeptide ( IAPP) to islet amyloid polypeptide ( IAPP<sub>22-28</sub>) oligomers.
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- Chemical Biology & Drug Design, 2017, v. 90, n. 1, p. 31, doi. 10.1111/cbdd.12924
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- Article
Revealing inhibition difference between PFI-2 enantiomers against SETD7 by molecular dynamics simulations, binding free energy calculations and unbinding pathway analysis.
- Published in:
- Scientific Reports, 2017, p. 46547, doi. 10.1038/srep46547
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- Article
Combined Ligand/Structure-Based Virtual Screening and Molecular Dynamics Simulations of Steroidal Androgen Receptor Antagonists.
- Published in:
- BioMed Research International, 2017, v. 2017, p. 1, doi. 10.1155/2017/3572394
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- Article
Molecular mechanism of R-bicalutamide switching from androgen receptor antagonist to agonist induced by amino acid mutations using molecular dynamics simulations and free energy calculation.
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- Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 12, p. 1189, doi. 10.1007/s10822-016-9992-2
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- Article
Protective V127 prion variant prevents prion disease by interrupting the formation of dimer and fibril from molecular dynamics simulations.
- Published in:
- Scientific Reports, 2016, p. 21804, doi. 10.1038/srep21804
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- Article
Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations.
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- PLoS ONE, 2015, v. 10, n. 12, p. 1, doi. 10.1371/journal.pone.0145219
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- Article
Ligand Efficiency Outperforms pIC<sub>50</sub> on Both 2D MLR and 3D CoMFA Models: A Case Study on AR Antagonists.
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- 2015
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- Publication type:
- Case Study
Effects of the Pathogenic Mutation A117V and the Protective Mutation H111S on the Folding and Aggregation of PrP106-126: Insights from Replica Exchange Molecular Dynamics Simulations.
- Published in:
- PLoS ONE, 2015, v. 10, n. 5, p. 1, doi. 10.1371/journal.pone.0125899
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- Article
The Molecular Mechanism of Bisphenol A (BPA) as an Endocrine Disruptor by Interacting with Nuclear Receptors: Insights from Molecular Dynamics (MD) Simulations.
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- PLoS ONE, 2015, v. 10, n. 3, p. 1, doi. 10.1371/journal.pone.0120330
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- Article
In Silico Study Combining Docking and QSAR Methods on a Series of Matrix Metalloproteinase 13 Inhibitors.
- Published in:
- Archiv der Pharmazie, 2014, v. 347, n. 11, p. 825, doi. 10.1002/ardp.201400200
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- Article