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Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant.
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- Journal of Computer-Aided Molecular Design, 2022, v. 36, n. 12, p. 879, doi. 10.1007/s10822-022-00487-w
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- Article
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: I. Standard procedure.
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- Journal of Computer-Aided Molecular Design, 2022, v. 36, n. 10, p. 735, doi. 10.1007/s10822-022-00475-0
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- Article
An Electrochemical Biosensor with Dual Signal Outputs: Toward Simultaneous Quantification of pH and O<sub>2</sub> in the Brain upon Ischemia and in a Tumor during Cancer Starvation Therapy.
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- Angewandte Chemie International Edition, 2017, v. 56, n. 35, p. 10471, doi. 10.1002/anie.201705615
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- Article
Selectivity of Neutral/Weakly Basic P1 Group Inhibitors of Thrombin and Trypsin by a Molecular Dynamics Study.
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- Chemistry - A European Journal, 2008, v. 14, n. 28, p. 8704, doi. 10.1002/chem.200800277
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- Article
Unveiling the gating mechanism of ECF Transporter RibU.
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- Scientific Reports, 2013, p. 1, doi. 10.1038/srep03566
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- Article
Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2.
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- Biomolecules (2218-273X), 2022, v. 12, n. 4, p. 572, doi. 10.3390/biom12040572
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- Article
Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq.
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- Biomolecules (2218-273X), 2021, v. 11, n. 11, p. 1653, doi. 10.3390/biom11111653
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- Article
Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations.
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- Nucleic Acids Research, 2019, v. 47, n. 13, p. 6618, doi. 10.1093/nar/gkz499
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- Article
Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation.
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- Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-19497-z
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- Article
Computational Characterization of Binding of Small Molecule Inhibitors to HIV-1 gp41.
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- Chinese Journal of Chemistry, 2011, v. 29, n. 7, p. 1307, doi. 10.1002/cjoc.201180241
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- Article
An Efficient Approach to the Accurate Prediction of Mutational Effects in Antigen Binding to the MHC1.
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- Molecules, 2024, v. 29, n. 4, p. 881, doi. 10.3390/molecules29040881
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- Article
DeepBindGCN: Integrating Molecular Vector Representation with Graph Convolutional Neural Networks for Protein–Ligand Interaction Prediction.
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- Molecules, 2023, v. 28, n. 12, p. 4691, doi. 10.3390/molecules28124691
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- Article
Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host–Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation.
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- Molecules, 2023, v. 28, n. 6, p. 2767, doi. 10.3390/molecules28062767
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- Article
Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion.
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- Molecules, 2021, v. 26, n. 11, p. 3120, doi. 10.3390/molecules26113120
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- Article
Full quantum mechanical study of binding of HIV-1 protease drugs.
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- International Journal of Quantum Chemistry, 2005, v. 103, n. 3, p. 246, doi. 10.1002/qua.20488
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- Article
Entropy driven cooperativity effect in multi-site drug optimization targeting SARS-CoV-2 papain-like protease.
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- Cellular & Molecular Life Sciences, 2023, v. 80, n. 11, p. 1, doi. 10.1007/s00018-023-04985-4
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- Article
Binding Modes of Small‐Molecule Inhibitors to the EED Pocket of PRC2.
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- ChemPhysChem, 2020, v. 21, n. 3, p. 263, doi. 10.1002/cphc.201900903
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- Article
Cover Feature: Rational Design of a Highly Specific Prolyl Endopeptidase To Activate the Antihypertensive Effect of Peptides (ChemBioChem 8/2023).
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- ChemBioChem, 2023, v. 24, n. 8, p. 1, doi. 10.1002/cbic.202300194
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- Article
Rational Design of a Highly Specific Prolyl Endopeptidase To Activate the Antihypertensive Effect of Peptides.
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- ChemBioChem, 2023, v. 24, n. 8, p. 1, doi. 10.1002/cbic.202200691
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- Article
Biosynthesis of eriodictyol in citrus waster by endowing P450BM3 activity of naringenin hydroxylation.
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- Applied Microbiology & Biotechnology, 2024, v. 108, n. 1, p. 1, doi. 10.1007/s00253-023-12867-9
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- Article
Biosynthesis of eriodictyol in citrus waster by endowing P450BM3 activity of naringenin hydroxylation.
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- Applied Microbiology & Biotechnology, 2024, v. 108, n. 1, p. 1, doi. 10.1007/s00253-023-12867-9
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- Article
SeBPPI: A Sequence-Based Protein–Protein Binding Predictor.
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- Journal of Computational Biophysics & Chemistry, 2022, v. 21, n. 6, p. 729, doi. 10.1142/S2737416522500314
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- Article
Interaction entropy for computational alanine scanning in protein–protein binding.
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- WIREs: Computational Molecular Science, 2018, v. 8, n. 2, p. 1, doi. 10.1002/wcms.1342
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- Article
Total and partial decay widths in vibrational predissociation of the HeI<sub>2</sub> van der Waals complex for lower initial vibrational excitations.
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- International Journal of Quantum Chemistry, 1997, v. 62, n. 1, p. 89, doi. 10.1002/(SICI)1097-461X(1997)62:1<89::AID-QUA9>3.0.CO;2-#
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- Article
Insights on Na<sup>+</sup> binding and conformational dynamics in multidrug and toxic compound extrusion transporter NorM.
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- Proteins, 2014, v. 82, n. 2, p. 240, doi. 10.1002/prot.24368
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- Article
Effect of Self-Assembly of Fullerene Nano-Particles on Lipid Membrane.
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- PLoS ONE, 2013, v. 8, n. 10, p. 1, doi. 10.1371/journal.pone.0077436
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- Article
BAR‐based optimum adaptive steered MD for configurational sampling.
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- Journal of Computational Chemistry, 2019, v. 40, n. 12, p. 1270, doi. 10.1002/jcc.25784
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- Article
Calculation of hot spots for protein–protein interaction in p53/PMI‐MDM2/MDMX complexes.
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- Journal of Computational Chemistry, 2019, v. 40, n. 9, p. 1045, doi. 10.1002/jcc.25592
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- Article
A new algorithm for construction of coarse-grained sites of large biomolecules.
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- Journal of Computational Chemistry, 2016, v. 37, n. 9, p. 795, doi. 10.1002/jcc.24265
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- Article
Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis.
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- Journal of Computational Chemistry, 2014, v. 35, n. 9, p. 737, doi. 10.1002/jcc.23547
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- Article
Discovery of novel inhibitors of CDK2 using docking and physics‐based binding free energy calculation.
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- Chemical Biology & Drug Design, 2022, v. 99, n. 5, p. 662, doi. 10.1111/cbdd.14027
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- Article
Analysis of the binding modes of the first‐ and second‐generation antiandrogens with respect to F876L mutation.
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- Chemical Biology & Drug Design, 2021, v. 98, n. 1, p. 60, doi. 10.1111/cbdd.13848
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- Article
Identification of three new compounds that directly target human serine hydroxymethyltransferase 2.
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- Chemical Biology & Drug Design, 2021, v. 97, n. 2, p. 221, doi. 10.1111/cbdd.13774
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- Article
HobPre: accurate prediction of human oral bioavailability for small molecules.
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- Journal of Cheminformatics, 2022, v. 14, n. 1, p. 1, doi. 10.1186/s13321-021-00580-6
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- Article
Effect of mismatch on binding of ADAR2/GluR-2 pre-mRNA complex.
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- Journal of Molecular Modeling, 2015, v. 21, n. 9, p. 1, doi. 10.1007/s00894-015-2760-8
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- Article
Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase.
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- Journal of Molecular Modeling, 2014, v. 20, n. 12, p. 1, doi. 10.1007/s00894-014-2530-z
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- Article
Novel theoretically designed HIV-1 non-nucleoside reverse transcriptase inhibitors derived from nevirapine.
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- Journal of Molecular Modeling, 2014, v. 20, n. 10, p. 1, doi. 10.1007/s00894-014-2451-x
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- Article
An Electrochemical Biosensor with Dual Signal Outputs: Toward Simultaneous Quantification of pH and O<sub>2</sub> in the Brain upon Ischemia and in a Tumor during Cancer Starvation Therapy.
- Published in:
- Angewandte Chemie, 2017, v. 129, n. 35, p. 10607, doi. 10.1002/ange.201705615
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- Publication type:
- Article
Revealing the Sequence Characteristics and Molecular Mechanisms of ACE Inhibitory Peptides by Comprehensive Characterization of 160,000 Tetrapeptides.
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- Foods, 2023, v. 12, n. 8, p. 1573, doi. 10.3390/foods12081573
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- Article
Crius: A novel fragment‐based algorithm of de novo substrate prediction for enzymes.
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- Protein Science: A Publication of the Protein Society, 2018, v. 27, n. 8, p. 1526, doi. 10.1002/pro.3437
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- Article
Screening and Analysis of Potential Inhibitors of SHMT2.
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- Biophysica, 2023, v. 3, n. 4, p. 651, doi. 10.3390/biophysica3040044
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- Publication type:
- Article
Revolutionizing GPCR–ligand predictions: DeepGPCR with experimental validation for high-precision drug discovery.
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- Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae281
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- Article
Generating and screening de novo compounds against given targets using ultrafast deep learning models as core components.
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- Briefings in Bioinformatics, 2022, v. 23, n. 4, p. 1, doi. 10.1093/bib/bbac226
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- Article
The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect.
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- Journal of Computational Chemistry, 2013, v. 34, n. 31, p. 2677, doi. 10.1002/jcc.23421
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- Article
Effect of Interprotein Polarization on Protein-Protein Binding Energy.
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- Journal of Computational Chemistry, 2012, v. 33, n. 16, p. 1416, doi. 10.1002/jcc.22969
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- Article
Electrostatic polarization is critical for the strong binding in streptavidin-biotin system.
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- Journal of Computational Chemistry, 2012, v. 33, n. 15, p. 1374, doi. 10.1002/jcc.22970
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- Publication type:
- Article
Global dynamics and transition state theories: Comparative study of reaction rate constants for gas-phase chemical reactions.
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- Journal of Computational Chemistry, 2009, v. 30, n. 2, p. 305, doi. 10.1002/jcc.21032
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- Article
Efficient bond function basis set for π-π interaction energies.
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- Journal of Computational Chemistry, 2008, v. 29, n. 2, p. 275, doi. 10.1002/jcc.20788
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- Article
Fully quantum mechanical energy optimization for protein-ligand structure.
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- Journal of Computational Chemistry, 2004, v. 25, n. 12, p. 1431, doi. 10.1002/jcc.20069
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- Article
Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations.
- Published in:
- Scientific Reports, 2017, p. 42223, doi. 10.1038/srep42223
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- Publication type:
- Article