Journal article |
- Claudio Perego; Raffaello Potestio. "Computational methods in the study of self-entangled proteins: a critical appraisal".
Journal of Physics: Condensed Matter (2019): https://doi.org/10.1088/1361-648X/ab2f19.
10.1088/1361-648X/ab2f19
- Maziar Heidari; Robinson Cortes-Huerto; Raffaello Potestio; Kurt Kremer. "Steering a solute between coexisting solvation states:
Revisiting nonequilibrium work relations and the calculation of free energy differences". The Journal of Chemical Physics
(2019): https://doi.org/10.1063/1.5117780.
10.1063/1.5117780
- Marco Giulini; Raffaello Potestio. "A deep learning approach to the structural analysis of proteins". Interface Focus
9 3 (2019): 20190003-20190003. https://doi.org/10.1098/rsfs.2019.0003.
10.1098/rsfs.2019.0003
- Enrico Riccardi; Sergio Pantano; Raffaello Potestio. "Envisioning data sharing for the biocomputing community". Interface
Focus 9 3 (2019): 20190005-20190005. https://doi.org/10.1098/rsfs.2019.0005.
10.1098/rsfs.2019.0005
- Radek Erban; Sarah Harris; Raffaello Potestio. "Multi-resolution simulations of intracellular processes". Interface Focus
9 3 (2019): 20190028-20190028. https://doi.org/10.1098/rsfs.2019.0028.
10.1098/rsfs.2019.0028
- Potestio, Raffaello. "Searching the Optimal Folding Routes of a Complex Lasso Protein". Biophysical Journal (2019):
http://dx.doi.org/10.1016/j.bpj.2019.05.025.
10.1016/j.bpj.2019.05.025
- Thomas Tarenzi; Vania Calandrini; Raffaello Potestio; Paolo Carloni. "Open-Boundary Molecular Mechanics/Coarse-Grained Framework
for Simulations of Low-Resolution G-Protein-Coupled Receptor–Ligand Complexes". Journal of Chemical Theory and Computation
15 3 (2019): 2101-2109. https://doi.org/10.1021/acs.jctc.9b00040.
10.1021/acs.jctc.9b00040
- Patrick Diggins, IV; Changjiang Liu; Markus Deserno; Raffaello Potestio. "Optimal Coarse-Grained Site Selection in Elastic
Network Models of Biomolecules". Journal of Chemical Theory and Computation 15 1 (2019): 648-664. https://doi.org/10.1021/acs.jctc.8b00654.
10.1021/acs.jctc.8b00654
- Maziar Heidari; Kurt Kremer; Robinson Cortes-Huerto; Raffaello Potestio. "Spatially Resolved Thermodynamic Integration: An
Efficient Method To Compute Chemical Potentials of Dense Fluids". Journal of Chemical Theory and Computation (2018):
https://doi.org/10.1021/acs.jctc.8b00002.
10.1021/acs.jctc.8b00002
- Maziar Heidari; Robinson Cortes-Huerto; Kurt Kremer; Raffaello Potestio. "Concurrent coupling of realistic and ideal models
of liquids and solids in Hamiltonian adaptive resolution simulations". The European Physical Journal E 41 5 (2018):
https://doi.org/10.1140%2Fepje%2Fi2018-11675-x.
10.1140/epje/i2018-11675-x
- Maziar Heidari; Kurt Kremer; Raffaello Potestio; Robinson Cortes-Huerto. "Fluctuations, Finite-Size Effects and the Thermodynamic
Limit in Computer Simulations: Revisiting the Spatial Block Analysis Method". Entropy 20 4 (2018): 222-222. https://doi.org/10.3390%2Fe20040222.
10.3390/e20040222
- Heidari, M.; Kremer, K.; Potestio, R.; Cortes-Huerto, R.. "Finite-size integral equations in the theory of liquids and the
thermodynamic limit in computer simulations". Molecular Physics 116 21-22 (2018): 3301-3310. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000444571600051&KeyUID=WOS:000444571600051.
10.1080/00268976.2018.1482429
- Karsten Kreis; Kurt Kremer; Raffaello Potestio; Mark E. Tuckerman. "From classical to quantum and back: Hamiltonian adaptive
resolution path integral, ring polymer, and centroid molecular dynamics". The Journal of Chemical Physics 147 24 (2017):
244104-244104. https://doi.org/10.1063/1.5000701.
10.1063/1.5000701
- Hamed Sharifi Dehsari; Maziar Heidari; Anielen Halda Ribeiro; Wolfgang Tremel; Gerhard Jakob; Davide Donadio; Raffaello Potestio;
Kamal Asadi. "Combined Experimental and Theoretical Investigation of Heating Rate on Growth of Iron Oxide Nanoparticles".
Chemistry of Materials 29 22 (2017): 9648-9656. https://doi.org/10.1021%2Facs.chemmater.7b02872.
10.1021/acs.chemmater.7b02872
- Thomas Tarenzi; Vania Calandrini; Raffaello Potestio; Alejandro Giorgetti; Paolo Carloni. "Open Boundary Simulations of Proteins
and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme". Journal of Chemical Theory and Computation 13
11 (2017): 5647-5657. https://doi.org/10.1021%2Facs.jctc.7b00508.
10.1021/acs.jctc.7b00508
- Raffaele Fiorentini; Kurt Kremer; Raffaello Potestio; Aoife C. Fogarty. "Using force-based adaptive resolution simulations
to calculate solvation free energies of amino acid sidechain analogues". The Journal of Chemical Physics 146 24 (2017):
244113-244113. https://doi.org/10.1063/1.4989486.
10.1063/1.4989486
- Aoife C. Fogarty; Raffaello Potestio; Kurt Kremer. "Erratum: “Adaptive resolution simulation of a biomolecule and its hydration
shell: Structural and dynamical properties” [J. Chem. Phys. 142, 195101 (2015)]". The Journal of Chemical Physics (2017):
10.1063/1.4975169
- Paulo A. Netz; Raffaello Potestio; Kurt Kremer. "Adaptive resolution simulation of oligonucleotides". The Journal of Chemical
Physics 145 23 (2016): 234101-234101. https://doi.org/10.1063/1.4972014.
10.1063/1.4972014
- Aoife C. Fogarty; Raffaello Potestio; Kurt Kremer. "A multi-resolution model to capture both global fluctuations of an enzyme
and molecular recognition in the ligand-binding site". Proteins: Structure, Function, and Bioinformatics 84 12 (2016):
1902-1913. https://doi.org/10.1002%2Fprot.25173.
10.1002/prot.25173
- Saeed Najafi; Rudolf Podgornik; Raffaello Potestio; Luca Tubiana. "Role of Bending Energy and Knot Chirality in Knot Distribution
and Their Effective Interaction along Stretched Semiflexible Polymers". Polymers 8 10 (2016): 347-347. https://doi.org/10.3390%2Fpolym8100347.
10.3390/polym8100347
- Najafi, Saeed; Tubiana, Luca; Podgornik, Rudolf; Potestio, Raffaello. "Chirality modifies the interaction between knots".
Epl 114 5 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000379525400007&KeyUID=WOS:000379525400007.
10.1209/0295-5075/114/50007
- Kreis, Karsten; Potestio, Raffaello; Kremer, Kurt; Fogarty, Aoife C. "Adaptive Resolution Simulations with Self-Adjusting
High-Resolution Regions.". Journal of chemical theory and computation 12 8 (2016): 4067-81. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:27384753&KeyUID=MEDLINE:27384753.
10.1021/acs.jctc.6b00440
- Kreis, Karsten; Tuckerman, Mark E.; Donadio, Davide; Kremer, Kurt; Potestio, Raffaello. "From Classical to Quantum and Back:
A Hamiltonian Scheme for Adaptive Multiresolution Classical/Path-Integral Simulations". Journal of Chemical Theory and
Computation 12 7 (2016): 3030-3039. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000379703800004&KeyUID=WOS:000379703800004.
10.1021/acs.jctc.6b00242
- Potestio, Raffaello; Tubiana, Luca. "Discretized knot motion on a tensioned fiber induced by transverse waves". Soft Matter
(2016):
10.1039/C5SM01766A
- Boereboom, Jelle M; Potestio, Raffaello; Donadio, Davide; Bulo, Rosa E. "Toward Hamiltonian Adaptive QM/MM: Accurate Solvent
Structures Using Many-Body Potentials.". Journal of chemical theory and computation 12 8 (2016): 3441-8. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:27332140&KeyUID=MEDLINE:27332140.
10.1021/acs.jctc.6b00205
- Kreis, Karsten; Potestio, Raffaello. "The relative entropy is fundamental to adaptive resolution simulations". Journal
of Chemical Physics 145 4 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000381679800006&KeyUID=WOS:000381679800006.
10.1063/1.4959169
- Raffaello Potestio; Luca Tubiana. "Discretized knot motion on a tensioned fiber induced by transverse waves". Soft Matter
12 3 (2016): 669-673. https://doi.org/10.1039%2Fc5sm01766a.
10.1039/c5sm01766a
- Heidari, M.; Cortes-Huerto, R.; Donadio, D.; Potestio, R.. "Accurate and general treatment of electrostatic interaction in
Hamiltonian adaptive resolution simulations". European Physical Journal-Special Topics 225 8-9 (2016): 1505-1526. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000386267000011&KeyUID=WOS:000386267000011.
10.1140/epjst/e2016-60151-6
- Cortes-Huerto, R.; Kremer, K.; Potestio, R.. "Communication: Kirkwood-Buff integrals in the thermodynamic limit from small-sized
molecular dynamics simulations". Journal of Chemical Physics 145 14 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000386535900004&KeyUID=WOS:000386535900004.
10.1063/1.4964779
- Kreis, K.; Fogarty, A. C.; Kremer, K.; Potestio, R.. "Advantages and challenges in coupling an ideal gas to atomistic models
in adaptive resolution simulations". European Physical Journal-Special Topics 224 12 (2015): 2289-2304. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000361371800007&KeyUID=WOS:000361371800007.
10.1140/epjst/e2015-02412-1
- Fogarty, Aoife C.; Potestio, Raffaello; Kremer, Kurt. "Adaptive resolution simulation of a biomolecule and its hydration shell:
Structural and dynamical properties". Journal of Chemical Physics 142 19 (2015): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000355006200044&KeyUID=WOS:000355006200044.
10.1063/1.4921347
- Kreis, K.; Fogarty, A. C.; Kremer, K.; Potestio, R.. "Reply to comments by R. Klein on Advantages and challenges in coupling
an ideal gas to atomistic models in adaptive resolution simulations". European Physical Journal-Special Topics 224
12 (2015): 2505-2506. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000361371800022&KeyUID=WOS:000361371800022.
10.1140/epjst/e2015-02533-5
- Najafi, Saeed; Potestio, Raffaello. "Folding of small knotted proteins: Insights from a mean field coarse-grained model".
Journal of Chemical Physics 143 24 (2015): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000370412900027&KeyUID=WOS:000370412900027.
10.1063/1.4934541
- Najafi, Saeed; Potestio, Raffaello. "Two Adhesive Sites Can Enhance the Knotting Probability of DNA". Plos One 10 7
(2015): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000358154400102&KeyUID=WOS:000358154400102.
10.1371/journal.pone.0132132
- Espanol, P.; Delgado-Buscalioni, R.; Everaers, R.; Potestio, R.; Donadio, D.; Kremer, K.. "Statistical mechanics of Hamiltonian
adaptive resolution simulations". Journal of Chemical Physics 142 6 (2015): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000349847000016&KeyUID=WOS:000349847000016.
10.1063/1.4907006
- Potestio, Raffaello. "Computer simulation of particles with position-dependent mass". European Physical Journal B 87
10 (2014): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000344168500003&KeyUID=WOS:000344168500003.
10.1140/epjb/e2014-50314-y
- Kreis, Karsten; Donadio, Davide; Kremer, Kurt; Potestio, Raffaello. "A unified framework for force-based and energy-based
adaptive resolution simulations". Epl 108 3 (2014): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000344913400007&KeyUID=WOS:000344913400007.
10.1209/0295-5075/108/30007
- Fritsch, Sebastian; Potestio, Raffaello; Donadio, Davide; Kremer, Kurt. "Nuclear Quantum Effects in Water: A Multiscale Study".
Journal of Chemical Theory and Computation 10 2 (2014): 816-824. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000331342400033&KeyUID=WOS:000331342400033.
10.1021/ct4010504
- Potestio, Raffaello; Peter, Christine; Kremer, Kurt. "Computer Simulations of Soft Matter: Linking the Scales". Entropy
16 8 (2014): 4199-4245. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000341215200002&KeyUID=WOS:000341215200002.
10.3390/e16084199
- Raffaello Potestio; Pep Español; Rafael Delgado-Buscalioni; Ralf Everaers; Kurt Kremer; Davide Donadio. "Monte Carlo Adaptive
Resolution Simulation of Multicomponent Molecular Liquids". Physical Review Letters 111 6 (2013): https://doi.org/10.1103%2Fphysrevlett.111.060601.
10.1103/physrevlett.111.060601
- Raffaello Potestio; Sebastian Fritsch; Pep Español; Rafael Delgado-Buscalioni; Kurt Kremer; Ralf Everaers; Davide Donadio.
"Hamiltonian Adaptive Resolution Simulation for Molecular Liquids". Physical Review Letters 110 10 (2013): https://doi.org/10.1103%2Fphysrevlett.110.108301.
10.1103/physrevlett.110.108301
- Polles, Guido; Indelicato, Giuliana; Potestio, Raffaello; Cermelli, Paolo; Twarock, Reidun; Micheletti, Cristian. "Mechanical
and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition". Plos Computational Biology 9
11 (2013): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000330357200031&KeyUID=WOS:000330357200031.
10.1371/journal.pcbi.1003331
- Potestio, Raffaello; Fritsch, Sebastian; Espanol, Pep; Delgado-Buscalioni, Rafael; Kremer, Kurt; Everaers, Ralf; Donadio,
Davide. "Hamiltonian Adaptive Resolution Simulation for Molecular Liquids". Physical Review Letters 110 10 (2013):
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000315744700026&KeyUID=WOS:000315744700026.
10.1103/PhysRevLett.110.108301
- Potestio, Raffaello; Espanol, Pep; Delgado-Buscalioni, Rafael; Everaers, Ralf; Kremer, Kurt; Donadio, Davide. "Monte Carlo
Adaptive Resolution Simulation of Multicomponent Molecular Liquids". Physical Review Letters 111 6 (2013): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000322921200004&KeyUID=WOS:000322921200004.
10.1103/PhysRevLett.111.060601
- Potestio, R.; Delle Site, L.. "Quantum locality and equilibrium properties in low-temperature parahydrogen: A multiscale simulation
study". Journal of Chemical Physics 136 5 (2012): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000300547200001&KeyUID=WOS:000300547200001.
10.1063/1.3678587
- Morra, Giulia; Potestio, Raffaello; Micheletti, Cristian; Colombo, Giorgio. "Corresponding Functional Dynamics across the
Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations". Plos Computational Biology 8 3 (2012):
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000302244000041&KeyUID=WOS:000302244000041.
10.1371/journal.pcbi.1002433
- Raffaello Potestio; Francesco Pontiggia; Tyanko Aleksiev; Stefano Cozzini; Cristian Micheletti. "Pisqrd: A Novel Variational
Scheme to Identify Dinamical Domains in Proteins". Biophysical Journal 98 3 (2010): 237a-237a. https://doi.org/10.1016%2Fj.bpj.2009.12.1283.
10.1016/j.bpj.2009.12.1283
- Potestio, Raffaello; Micheletti, Cristian; Orland, Henri. "Knotted vs. Unknotted Proteins: Evidence of Knot-Promoting Loops".
Plos Computational Biology 6 7 (2010): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000280528300033&KeyUID=WOS:000280528300033.
10.1371/journal.pcbi.1000864
- Potestio, R.; Aleksiev, T.; Pontiggia, F.; Cozzini, S.; Micheletti, C.. "ALADYN: a web server for aligning proteins by matching
their large-scale motion". Nucleic Acids Research 38 (2010): W41-W45. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000284148900008&KeyUID=WOS:000284148900008.
10.1093/nar/gkq293
- Aleksiev, T.; Potestio, R.; Pontiggia, F.; Cozzini, S.; Micheletti, C.. "PiSQRD: a web server for decomposing proteins into
quasi-rigid dynamical domains". Bioinformatics 25 20 (2009): 2743-2744. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000270685200021&KeyUID=WOS:000270685200021.
10.1093/bioinformatics/btp512
- Potestio, R.; Pontiggia, F.; Micheletti, C.. "Coarse-Grained Description of Protein Internal Dynamics: An Optimal Strategy
for Decomposing Proteins in Rigid Subunits". Biophysical Journal 96 12 (2009): 4993-5002. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000267194600024&KeyUID=WOS:000267194600024.
10.1016/j.bpj.2009.03.051
- Potestio, Raffaello; Caccioli, Fabio; Vivo, Pierpaolo. "Random Matrix Approach to Collective Behavior and Bulk Universality
in Protein Dynamics". Physical Review Letters 103 26 (2009): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000273232200052&KeyUID=WOS:000273232200052.
10.1103/PhysRevLett.103.268101
- Raffaello Potestio; Fabio Caccioli; Pierpaolo Vivo. "Random Matrix Approach to Collective Behavior and Bulk Universality in
Protein Dynamics". Physical Review Letters 103 26 (2009): https://doi.org/10.1103%2Fphysrevlett.103.268101.
10.1103/physrevlett.103.268101
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