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A Model for the Rapid Assessment of Solution Structures for 24-Atom Macrocycles: The Impact of β-Branched Amino Acids on Conformation
2023 Menke, A. J.; Gloor, C. J.; Claton, L. E.; Mekhail, M. A.; Pan, H.; Stewart, M. D.; Green, K. N.; Reibenspies, J. H.; Pavan, G. M.; Capelli, R.; Simanek, E. E.
Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG
2023 Empereur-mot, Charly; Pedersen, Kasper B.; Capelli, Riccardo; Crippa, Martina; Caruso, Cristina; Perrone, Mattia; Souza, Paulo C. T.; Marrink, Siewert J.; Pavan, Giovanni M.
Automatic multi-objective optimization of coarse-grained lipid force fields using SwarmCG
2022 Empereur-mot, Charly; Capelli, Riccardo; Perrone, Mattia; Caruso, Cristina; Doni, Giovanni; Pavan, Giovanni M.
Controlling the length of porphyrin supramolecular polymers via coupled equilibria and dilution-induced supramolecular polymerization
2022 Weyandt, Elisabeth; Leanza, Luigi; Capelli, Riccardo; Pavan, Giovanni M.; Vantomme, Ghislaine; Meijer, E. W.
Density-tunable pathway complexity in a minimalistic self-assembly model
2022 Becchi, Matteo; Capelli, Riccardo; Perego, Claudio; Pavan, Giovanni M.; Micheletti, Cristian
Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective
2022 Ahmad, Katya; Rizzi, Andrea; Capelli, Riccardo; Mandelli, Davide; Lyu, Wenping; Carloni, Paolo
Ephemeral ice-like local environments in classical rigid models of liquid water
2022 Capelli, R.; Muniz-Miranda, F.; Pavan, G. M.
Multiple Poses and Thermodynamics of Ligands Targeting Protein Surfaces: The Case of Furosemide Binding to mitoNEET in Aqueous Solution
2022 Hoang, Linh Gia; Goßen, Jonas; Capelli, Riccardo; Nguyen, Toan T.; Sun, Zhaoxi; Zuo, Ke; Schulz, Jörg B.; Rossetti, Giulia; Carloni, Paolo
Porous covalent organic nanotubes and their assembly in loops and toroids
2022 Koner, Kalipada; Karak, Shayan; Kandambeth, Sharath; Karak, Suvendu; Thomas, Neethu; Leanza, Luigi; Perego, Claudio; Pesce, Luca; Capelli, Riccardo; Moun, Monika; Bhakar, Monika; Ajithkumar, Thalasseril G.; Pavan, Giovanni M.; Banerjee, Rahul
Well-Tempered Metadynamics Simulations Predict the Structural and Dynamic Properties of a Chiral 24-Atom Macrocycle in Solution
2022 Capelli, Riccardo; Menke, Alexander J.; Pan, Hongjun; Janesko, Benjamin G.; Simanek, Eric E.; Pavan, Giovanni M.
A Data-Driven Dimensionality Reduction Approach to Compare and Classify Lipid Force Fields
2021 Capelli, Riccardo; Gardin, Andrea; Empereur-mot, Charly; Doni, Giovanni; Pavan, Giovanni M.
Enhanced sampling approach to the induced-fit docking problem in protein-ligand binding: the Case of mono-ADP-ribosylation hydrolase inhibitors
2021 Zhao, Qianqian; Capelli, Riccardo; Carloni, Paolo; Lüscher, Bernhard; Li, Jinyu; Rossetti, Giulia
Evolution of frustrated and stabilising contacts in reconstructed ancient proteins
2021 Crippa, M.; Andreghetti, D.; Capelli, R.; Tiana, G.
Multiscale Molecular Modelling of ATP‐Fueled Supramolecular Polymerisation and Depolymerisation
2021 Perego, Claudio; Pesce, Luca; Capelli, Riccardo; George, Subi J.; Pavan, Giovanni M.
Accuracy of Molecular Simulation-Based Predictions of koff Values: A Metadynamics Study
2020 Capelli, R.; Lyu, W.; Bolnykh, V.; Meloni, S.; Olsen, J. M. H.; Rothlisberger, U.; Parrinello, M.; Carloni, P.
Coevolutionary data-based interaction networks approach highlighting key residues across protein families: The case of the G-protein coupled receptors
2020 Baldessari, Filippo; Capelli, Riccardo; Carloni, Paolo; Giorgetti, Alejandro
Cooperative Supramolecular Block Copolymerization for the Synthesis of Functional Axial Organic Heterostructures
2020 Sarkar, A.; Behera, T.; Sasmal, R.; Capelli, R.; Empereur-Mot, C.; Mahato, J.; Agasti, S. S.; Pavan, G. M.; Chowdhury, A.; George, S. J.
Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization
2020 Empereur-Mot, Charly; Pesce, Luca; Doni, Giovanni; Bochicchio, Davide; Capelli, Riccardo; Perego, Claudio; Pavan, Giovanni M.
| Citazione | Data di pubblicazione | Autori | File |
|---|---|---|---|
| A Model for the Rapid Assessment of Solution Structures for 24-Atom Macrocycles: The Impact of β-Branched Amino Acids on Conformation / Menke, A. J.; Gloor, C. J.; Claton, L. E.; Mekhail, M. A.; Pan, H.; Stewart, M. D.; Green, K. N.; Reibenspies, J. H.; Pavan, G. M.; Capelli, R.; Simanek, E. E.. - In: JOURNAL OF ORGANIC CHEMISTRY. - ISSN 0022-3263. - 88:5(2023), pp. 2692-2702. [10.1021/acs.joc.2c01984] | 1-gen-2023 | Pavan G. M.Capelli R. + | Menke et al GIVT to JOC.pdf; acs.joc.2c01984.pdf |
| Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG / Empereur-mot, Charly; Pedersen, Kasper B.; Capelli, Riccardo; Crippa, Martina; Caruso, Cristina; Perrone, Mattia; Souza, Paulo C. T.; Marrink, Siewert J.; Pavan, Giovanni M.. - In: JOURNAL OF CHEMICAL INFORMATION AND MODELING. - ISSN 1549-9596. - 63:12(2023), pp. 3827-3838. [10.1021/acs.jcim.3c00530] | 1-gen-2023 | Riccardo CapelliMartina CrippaCristina CarusoMattia PerroneGiovanni M. Pavan + | acs.jcim.3c00530_compressed.pdf |
| Automatic multi-objective optimization of coarse-grained lipid force fields using SwarmCG / Empereur-mot, Charly; Capelli, Riccardo; Perrone, Mattia; Caruso, Cristina; Doni, Giovanni; Pavan, Giovanni M.. - In: THE JOURNAL OF CHEMICAL PHYSICS. - ISSN 0021-9606. - ELETTRONICO. - 156:2(2022), p. 024801. [10.1063/5.0079044] | 1-gen-2022 | Riccardo CapelliMattia PerroneCristina CarusoGiovanni M. Pavan + | JCP21-AR-04102.pdf; JCP-SwarmCG_compressed.pdf |
| Controlling the length of porphyrin supramolecular polymers via coupled equilibria and dilution-induced supramolecular polymerization / Weyandt, Elisabeth; Leanza, Luigi; Capelli, Riccardo; Pavan, Giovanni M.; Vantomme, Ghislaine; Meijer, E. W.. - In: NATURE COMMUNICATIONS. - ISSN 2041-1723. - ELETTRONICO. - 13:1(2022), p. 248. [10.1038/s41467-021-27831-2] | 1-gen-2022 | Luigi LeanzaRiccardo CapelliGiovanni M. Pavan + | s41467-021-27831-2.pdf |
| Density-tunable pathway complexity in a minimalistic self-assembly model / Becchi, Matteo; Capelli, Riccardo; Perego, Claudio; Pavan, Giovanni M.; Micheletti, Cristian. - In: SOFT MATTER. - ISSN 1744-683X. - 18:(2022), pp. 8106-8116. [10.1039/D2SM00968D] | 1-gen-2022 | Becchi,MatteoCapelli,RiccardoPavan,Giovanni M. + | Becchietal2022-postprint-accepted.pdf; Becchietal2022-postprint-published.pdf |
| Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective / Ahmad, Katya; Rizzi, Andrea; Capelli, Riccardo; Mandelli, Davide; Lyu, Wenping; Carloni, Paolo. - In: FRONTIERS IN MOLECULAR BIOSCIENCES. - ISSN 2296-889X. - ELETTRONICO. - 9:(2022), p. 899805. [10.3389/fmolb.2022.899805] | 1-gen-2022 | Riccardo Capelli + | fmolb-09-899805.pdf |
| Ephemeral ice-like local environments in classical rigid models of liquid water / Capelli, R.; Muniz-Miranda, F.; Pavan, G. M.. - In: THE JOURNAL OF CHEMICAL PHYSICS. - ISSN 0021-9606. - ELETTRONICO. - 156:21(2022), p. 214503. [10.1063/5.0088599] | 1-gen-2022 | Capelli R.Pavan G. M. + | 5.0088599.pdf; JCP22-AR-00618.pdf |
| Multiple Poses and Thermodynamics of Ligands Targeting Protein Surfaces: The Case of Furosemide Binding to mitoNEET in Aqueous Solution / Hoang, Linh Gia; Goßen, Jonas; Capelli, Riccardo; Nguyen, Toan T.; Sun, Zhaoxi; Zuo, Ke; Schulz, Jörg B.; Rossetti, Giulia; Carloni, Paolo. - In: FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY. - ISSN 2296-634X. - ELETTRONICO. - 10:(2022). [10.3389/fcell.2022.886568] | 1-gen-2022 | Capelli, Riccardo + | fcell-10-886568.pdf |
| Porous covalent organic nanotubes and their assembly in loops and toroids / Koner, Kalipada; Karak, Shayan; Kandambeth, Sharath; Karak, Suvendu; Thomas, Neethu; Leanza, Luigi; Perego, Claudio; Pesce, Luca; Capelli, Riccardo; Moun, Monika; Bhakar, Monika; Ajithkumar, Thalasseril G.; Pavan, Giovanni M.; Banerjee, Rahul. - In: NATURE CHEMISTRY. - ISSN 1755-4330. - ELETTRONICO. - (2022). [10.1038/s41557-022-00908-1] | 1-gen-2022 | Luigi LeanzaRiccardo CapelliGiovanni M. Pavan + | Accepted-Version.pdf; s41557-022-00908-1_compressed.pdf |
| Well-Tempered Metadynamics Simulations Predict the Structural and Dynamic Properties of a Chiral 24-Atom Macrocycle in Solution / Capelli, Riccardo; Menke, Alexander J.; Pan, Hongjun; Janesko, Benjamin G.; Simanek, Eric E.; Pavan, Giovanni M.. - In: ACS OMEGA. - ISSN 2470-1343. - ELETTRONICO. - 7:34(2022), pp. 30291-30296. [10.1021/acsomega.2c03536] | 1-gen-2022 | Riccardo CapelliGiovanni M. Pavan + | acsomega.2c03536.pdf |
| A Data-Driven Dimensionality Reduction Approach to Compare and Classify Lipid Force Fields / Capelli, Riccardo; Gardin, Andrea; Empereur-mot, Charly; Doni, Giovanni; Pavan, Giovanni M.. - In: JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL. - ISSN 1520-6106. - ELETTRONICO. - (2021). [10.1021/acs.jpcb.1c02503] | 1-gen-2021 | Riccardo CapelliAndrea GardinGiovanni M. Pavan + | acs.jpcb.1c02503.pdf |
| Enhanced sampling approach to the induced-fit docking problem in protein-ligand binding: the Case of mono-ADP-ribosylation hydrolase inhibitors / Zhao, Qianqian; Capelli, Riccardo; Carloni, Paolo; Lüscher, Bernhard; Li, Jinyu; Rossetti, Giulia. - In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. - ISSN 1549-9618. - ELETTRONICO. - 17:12(2021), pp. 7899-7911. | 1-gen-2021 | Capelli,Riccardo + | acs.jctc.1c00649.pdf |
| Evolution of frustrated and stabilising contacts in reconstructed ancient proteins / Crippa, M.; Andreghetti, D.; Capelli, R.; Tiana, G.. - In: EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS. - ISSN 0175-7571. - ELETTRONICO. - 50:5(2021), pp. 699-712. [10.1007/s00249-021-01500-0] | 1-gen-2021 | Crippa M.Capelli R. + | Crippa2021_Article_EvolutionOfFrustratedAndStabil-2.pdf |
| Multiscale Molecular Modelling of ATP‐Fueled Supramolecular Polymerisation and Depolymerisation / Perego, Claudio; Pesce, Luca; Capelli, Riccardo; George, Subi J.; Pavan, Giovanni M.. - In: CHEMSYSTEMSCHEM. - ISSN 2570-4206. - 3:e2000038(2021). [10.1002/syst.202000038] | 1-gen-2021 | Capelli, RiccardoPavan, Giovanni M. + | chem_sys_chem_2020-Draft.pdf; syst.202000038.pdf; manuscript.pdf; supporting_information.pdf |
| Accuracy of Molecular Simulation-Based Predictions of koff Values: A Metadynamics Study / Capelli, R.; Lyu, W.; Bolnykh, V.; Meloni, S.; Olsen, J. M. H.; Rothlisberger, U.; Parrinello, M.; Carloni, P.. - In: THE JOURNAL OF PHYSICAL CHEMISTRY LETTERS. - ISSN 1948-7185. - 11:15(2020), pp. 6373-6381. [10.1021/acs.jpclett.0c00999] | 1-gen-2020 | Capelli R. + | receptor.pdf; jz0c00999_si_001.pdf; LaTeX_JPCLetters-2.pdf |
| Coevolutionary data-based interaction networks approach highlighting key residues across protein families: The case of the G-protein coupled receptors / Baldessari, Filippo; Capelli, Riccardo; Carloni, Paolo; Giorgetti, Alejandro. - In: COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL. - ISSN 2001-0370. - ELETTRONICO. - 18:(2020), pp. 1153-1159. [10.1016/j.csbj.2020.05.003] | 1-gen-2020 | Capelli, Riccardo + | 1-s2.0-S200103702030266X-main-2.pdf |
| Cooperative Supramolecular Block Copolymerization for the Synthesis of Functional Axial Organic Heterostructures / Sarkar, A.; Behera, T.; Sasmal, R.; Capelli, R.; Empereur-Mot, C.; Mahato, J.; Agasti, S. S.; Pavan, G. M.; Chowdhury, A.; George, S. J.. - In: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. - ISSN 0002-7863. - 142:26(2020), pp. 11528-11539. [10.1021/jacs.0c04404] | 1-gen-2020 | Capelli R.Pavan G. M. + | supramolecular.pdf; ja0c04404_si_001.pdf; subi2.pdf; JACS_10.1021:jacs.0c04404.pdf |
| Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization / Empereur-Mot, Charly; Pesce, Luca; Doni, Giovanni; Bochicchio, Davide; Capelli, Riccardo; Perego, Claudio; Pavan, Giovanni M.. - In: ACS OMEGA. - ISSN 2470-1343. - (2020). [10.1021/acsomega.0c05469] | 1-gen-2020 | Riccardo CapelliGiovanni M. Pavan + | acsomega.0c05469.pdf |