| Year |
Title |
| 2024
|
Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface..
Journal of Chemical Information and Modeling.
64:2068-2076.
2024
|
| 2024
|
Interactions and Transport of a Bioconjugated Peptide Targeting the Mitomembrane..
Bioconjugate Chemistry.
35:371-380.
2024
|
| 2024
|
Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinases..
Proteins: Structure, Function, and Bioinformatics.
2024
|
| 2024
|
Porous Self-Assemblies Mediated by Dumbbell Particles as Cross-Linking Agents..
Journal of Chemical Theory and Computation.
20:1590-1599.
2024
|
| 2024
|
Self-Assembly in an Experimentally Realistic Model of Lobed Patchy Colloids..
ACS Appl Bio Mater.
7:535-542.
2024
|
| 2024
|
Structural and computational studies of HIV-1 RNA..
RNA Biology.
21:1-32.
2024
|
| 2023
|
Mechanism of Ligand Discrimination by the NMT1 Riboswitch..
Journal of Chemical Information and Modeling.
63:4864-4874.
2023
|
| 2023
|
Coupling of conformational dynamics and inhibitor binding in the phosphodiesterase-5 family..
Protein Science.
32:e4720.
2023
|
| 2023
|
Role of Dynamics and Mutations in Interactions of a Zinc Finger Antiviral Protein with CG-rich Viral RNA..
Journal of Chemical Information and Modeling.
63:1002-1011.
2023
|
| 2023
|
Structural models of viral insulin-like peptides and their analogs..
Proteins: Structure, Function, and Bioinformatics.
91:62-73.
2023
|
| 2022
|
Molecular interactions and inhibition of the SARS-CoV-2 main protease by a thiadiazolidinone derivative..
Proteins: Structure, Function, and Bioinformatics.
90:1896-1907.
2022
|
| 2022
|
Epitaxial Self-Assembly of Interfaces of 2D Metal-Organic Frameworks for Electroanalytical Detection of Neurotransmitters..
ACS Nano.
16:13869-13883.
2022
|
| 2022
|
Role of Mutations in Differential Recognition of Viral RNA Molecules by Peptides..
Journal of Chemical Information and Modeling.
62:3381-3390.
2022
|
| 2022
|
Self-Assembly in Mixtures of Charged Lobed Particles.
Frontiers in Physics.
10.
2022
|
| 2022
|
Cover Image, Volume 90, Issue 3.
Proteins: Structure, Function, and Bioinformatics.
90.
2022
|
| 2022
|
Structures and interactions of insulin-like peptides from cone snail venom..
Proteins: Structure, Function, and Bioinformatics.
90:680-690.
2022
|
| 2022
|
Progress in Simulation Studies of Insulin Structure and Function..
Frontiers in Endocrinology.
13:908724.
2022
|
| 2021
|
Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides..
Biophysical Journal.
120:5060-5073.
2021
|
| 2021
|
Conformational dynamics and energetics of viral RNA recognition by lab-evolved proteins..
Physical Chemistry Chemical Physics.
23:24773-24779.
2021
|
| 2021
|
Self-Assembly of Porous Structures From a Binary Mixture of Lobed Patchy Particles.
Frontiers in Physics.
9.
2021
|
| 2021
|
Design of Functionalized Lobed Particles for Porous Self-Assemblies.
Journal of Metals.
73:2413-2422.
2021
|
| 2021
|
Liposome-based measurement of light-driven chloride transport kinetics of halorhodopsin..
BBA: Biomembranes.
1863:183637.
2021
|
| 2021
|
Role of conformational heterogeneity in ligand recognition by viral RNA molecules..
Physical Chemistry Chemical Physics.
23:11211-11223.
2021
|
| 2021
|
Enhanced Porosity in Self-Assembled Morphologies Mediated by Charged Lobes on Patchy Particles..
The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter.
125:3208-3215.
2021
|
| 2021
|
Reaction Coordinate and Thermodynamics of Base Flipping in RNA..
Journal of Chemical Theory and Computation.
17:1914-1921.
2021
|
| 2021
|
Allosteric Pathways Originating at Cysteine Residues in Regulators of G-Protein Signaling Proteins..
Biophysical Journal.
120:517-526.
2021
|
| 2021
|
Water Dynamics in a Peptide-appended Pillar[5]arene Artificial Channel in Lipid and Biomimetic Membranes..
Frontiers in Chemistry.
9:753635.
2021
|
| 2020
|
Structural Analysis of the Regulatory GAF Domains of cGMP Phosphodiesterase Elucidates the Allosteric Communication Pathway..
Journal of Molecular Biology.
432:5765-5783.
2020
|
| 2020
|
Self-assembly behavior of experimentally realizable lobed patchy particles..
Soft Matter.
16:8101-8107.
2020
|
| 2020
|
Role of Entropy in Colloidal Self-Assembly..
Entropy: international and interdisciplinary journal of entropy and information studies.
22:E877.
2020
|
| 2020
|
Ligand Recognition in Viral RNA Necessitates Rare Conformational Transitions..
Journal of Physical Chemistry Letters.
11:5426-5432.
2020
|
| 2020
|
Functional Nanoassemblies with Mirror-Image Chiroptical Properties Templated by a Single Homochiral DNA Strand.
Chemistry of Materials.
32:2272-2281.
2020
|
| 2020
|
Self-assembly of lobed particles into amorphous and crystalline porous structures..
Soft Matter.
16:1142-1147.
2020
|
| 2019
|
An Interhelical Salt Bridge Controls Flexibility and Inhibitor Potency for Regulators of G-protein Signaling Proteins 4, 8, and 19..
Molecular Pharmacology.
96:683-691.
2019
|
| 2019
|
Conformational dynamics and interfacial interactions of peptide-appended pillar[5]arene water channels in biomimetic membranes..
Physical Chemistry Chemical Physics.
21:22711-22721.
2019
|
| 2019
|
Phase space and collective variable based simulation methods for studies of rare events.
Molecular Simulation.
45:1273-1284.
2019
|
| 2019
|
Interplay of cysteine exposure and global protein dynamics in small-molecule recognition by a regulator of G-protein signaling protein..
Proteins: Structure, Function, and Bioinformatics.
87:146-156.
2019
|
| 2019
|
Pharmacological and molecular dynamics analyses of differences in inhibitor binding to human and nematode PDE4: Implications for management of parasitic nematodes..
PLoS ONE.
14:e0214554.
2019
|
| 2018
|
Diffusion network of CO in FeFe-Hydrogenase..
Journal of Chemical Physics.
149:204108.
2018
|
| 2018
|
Interpreting Hydrogen-Deuterium Exchange Events in Proteins Using Atomistic Simulations: Case Studies on Regulators of G-Protein Signaling Proteins..
The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter.
122:9314-9323.
2018
|
| 2018
|
Applications to water transport systems: general discussion..
Faraday Discussions.
209:389-414.
2018
|
| 2018
|
Biomimetic water channels: general discussion..
Faraday Discussions.
209:205-229.
2018
|
| 2018
|
Parameterization and atomistic simulations of biomimetic membranes..
Faraday Discussions.
209:161-178.
2018
|
| 2018
|
Structure and function of natural proteins for water transport: general discussion..
Faraday Discussions.
209:83-95.
2018
|
| 2018
|
The modelling and enhancement of water hydrodynamics: general discussion..
Faraday Discussions.
209:273-285.
2018
|
| 2018
|
Achieving high permeability and enhanced selectivity for Angstrom-scale separations using artificial water channel membranes..
Nature Communications.
9:2294.
2018
|
| 2018
|
Differential Protein Dynamics of Regulators of G-Protein Signaling: Role in Specificity of Small-Molecule Inhibitors..
Journal of the American Chemical Society.
140:3454-3460.
2018
|
| 2017
|
Pathways and Thermodynamics of Oxygen Diffusion in [FeFe]-Hydrogenase..
The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter.
121:10007-10017.
2017
|
| 2017
|
Insulin mimetic peptide S371 folds into a helical structure..
Journal of Computational Chemistry.
38:1158-1166.
2017
|
| 2017
|
Kinetics of Ligand Binding Through Advanced Computational Approaches: A Review..
Current Topics in Medicinal Chemistry.
17:2626-2641.
2017
|
| 2016
|
All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors..
Frontiers in Endocrinology.
7:68.
2016
|
| 2015
|
Theoretical and computational studies of peptides and receptors of the insulin family..
Membranes.
5:48-83.
2015
|
| 2014
|
Flexibility in the insulin receptor ectodomain enables docking of insulin in crystallographic conformation observed in a hormone-bound microreceptor..
Membranes.
4:730-746.
2014
|
| 2014
|
Collective variable approaches for single molecule flexible fitting and enhanced sampling..
Chemical Reviews.
114:3353-3365.
2014
|
| 2013
|
Conformational dynamics of a regulator of G-protein signaling protein reveals a mechanism of allosteric inhibition by a small molecule..
ACS Chemical Biology.
8:2778-2784.
2013
|
| 2013
|
All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element..
Proteins: Structure, Function, and Bioinformatics.
81:1017-1030.
2013
|
| 2013
|
Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps..
The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter.
117:3738-3746.
2013
|
| 2012
|
Conformational Sampling of Maltose-transporter Components in Cartesian Collective Variables is Governed by the Low-frequency Normal Modes..
Journal of Physical Chemistry Letters.
3:3379-3384.
2012
|
| 2012
|
Using enhanced sampling and structural restraints to refine atomic structures into low-resolution electron microscopy maps..
Structure.
20:1453-1462.
2012
|
| 2012
|
"DFG-flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop..
Biophysical Journal.
102:1979-1987.
2012
|
| 2011
|
Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates..
Science.
333:1449-1453.
2011
|
| 2010
|
All-atom structural models for complexes of insulin-like growth factors IGF1 and IGF2 with their cognate receptor..
Journal of Molecular Biology.
400:645-658.
2010
|
| 2010
|
Docking of insulin to a structurally equilibrated insulin receptor ectodomain..
Proteins: Structure, Function, and Bioinformatics.
78:1531-1543.
2010
|
| 2008
|
Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex..
Biophysical Journal.
95:4193-4204.
2008
|
| |
Characterization of water dynamics in sub-nm pore-size biomimetic membranes.
Journal of Physical Chemistry Letters.
|
| |
Flux and pathways in model potentials.
Molecular Simulation.
|
