Year |
Citation |
Score |
2023 |
Majewski M, Pérez A, Thölke P, Doerr S, Charron NE, Giorgino T, Husic BE, Clementi C, Noé F, De Fabritiis G. Machine learning coarse-grained potentials of protein thermodynamics. Nature Communications. 14: 5739. PMID 37714883 DOI: 10.1038/s41467-023-41343-1 |
0.387 |
|
2023 |
Conev A, Rigo MM, Devaurs D, Fonseca AF, Kalavadwala H, de Freitas MV, Clementi C, Zanatta G, Antunes DA, Kavraki LE. EnGens: a computational framework for generation and analysis of representative protein conformational ensembles. Briefings in Bioinformatics. 24. PMID 37418278 DOI: 10.1093/bib/bbad242 |
0.385 |
|
2023 |
Conev A, Rigo MM, Devaurs D, Fonseca AF, Kalavadwala H, de Freitas MV, Clementi C, Zanatta G, Antunes DA, Kavraki L. EnGens: a computational framework for generation and analysis of representative protein conformational ensembles. Biorxiv : the Preprint Server For Biology. PMID 37163076 DOI: 10.1101/2023.04.24.538094 |
0.384 |
|
2020 |
Abella JR, Antunes DA, Clementi C, Kavraki LE. Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests. Frontiers in Immunology. 11: 1583. PMID 32793224 DOI: 10.3389/Fimmu.2020.01583 |
0.32 |
|
2020 |
Noé F, Tkatchenko A, Müller KR, Clementi C. Machine Learning for Molecular Simulation. Annual Review of Physical Chemistry. PMID 32092281 DOI: 10.1146/Annurev-Physchem-042018-052331 |
0.363 |
|
2020 |
Wang J, Chmiela S, Müller K, Noé F, Clementi C. Ensemble learning of coarse-grained molecular dynamics force fields with a kernel approach The Journal of Chemical Physics. 152: 194106. DOI: 10.1063/5.0007276 |
0.302 |
|
2020 |
Klus S, Nüske F, Peitz S, Niemann J, Clementi C, Schütte C. Data-driven approximation of the Koopman generator: Model reduction, system identification, and control Physica D: Nonlinear Phenomena. 406: 132416. DOI: 10.1016/J.Physd.2020.132416 |
0.352 |
|
2019 |
Noé F, De Fabritiis G, Clementi C. Machine learning for protein folding and dynamics. Current Opinion in Structural Biology. 60: 77-84. PMID 31881449 DOI: 10.1016/J.Sbi.2019.12.005 |
0.393 |
|
2019 |
Lehmann M, Lukonin I, Noé F, Schmoranzer J, Clementi C, Loerke D, Haucke V. Nanoscale coupling of endocytic pit growth and stability. Science Advances. 5: eaax5775. PMID 31807703 DOI: 10.1126/Sciadv.Aax5775 |
0.303 |
|
2019 |
Nüske F, Boninsegna L, Clementi C. Coarse-graining molecular systems by spectral matching. The Journal of Chemical Physics. 151: 044116. PMID 31370528 DOI: 10.1063/1.5100131 |
0.405 |
|
2019 |
Wang J, Olsson S, Wehmeyer C, Pérez A, Charron NE, de Fabritiis G, Noé F, Clementi C. Machine Learning of Coarse-Grained Molecular Dynamics Force Fields. Acs Central Science. 5: 755-767. PMID 31139712 DOI: 10.1021/Acscentsci.8B00913 |
0.395 |
|
2019 |
Chen J, Schafer NP, Wolynes PG, Clementi C. Localizing Frustration in Proteins Using All-Atom Energy Functions. The Journal of Physical Chemistry. B. PMID 31063375 DOI: 10.1021/Acs.Jpcb.9B01545 |
0.424 |
|
2019 |
Pettini G, Gori M, Franzosi R, Clementi C, Pettini M. On the origin of phase transitions in the absence of symmetry-breaking Physica a: Statistical Mechanics and Its Applications. 516: 376-392. DOI: 10.1016/J.Physa.2018.10.001 |
0.303 |
|
2019 |
Clementi C. Multiscale Modeling of Biomolecular Processes by Combining Experiment and Simulation Biophysical Journal. 116: 34a. DOI: 10.1016/J.Bpj.2018.11.226 |
0.314 |
|
2018 |
Hruska E, Abella JR, Nüske F, Kavraki LE, Clementi C. Quantitative comparison of adaptive sampling methods for protein dynamics. The Journal of Chemical Physics. 149: 244119. PMID 30599712 DOI: 10.1063/1.5053582 |
0.407 |
|
2018 |
Yrazu FM, Pinamonti G, Clementi C. The Effect of Electrostatic Interactions on the Folding Kinetics of a 3-α-Helical Bundle Protein Family. The Journal of Physical Chemistry. B. PMID 30277393 DOI: 10.1021/Acs.Jpcb.8B08676 |
0.434 |
|
2018 |
Pinamonti G, Campo G, Chen J, Kluber A, Clementi C. Simulations Reveal Multiple Intermediates in the Unzipping Mechanism of Neuronal SNARE Complex. Biophysical Journal. PMID 30268539 DOI: 10.1016/J.Bpj.2018.08.043 |
0.43 |
|
2018 |
Kluber A, Burt TA, Clementi C. Size and topology modulate the effects of frustration in protein folding. Proceedings of the National Academy of Sciences of the United States of America. PMID 30150375 DOI: 10.1073/Pnas.1801406115 |
0.465 |
|
2018 |
Boninsegna L, Nüske F, Clementi C. Sparse learning of stochastic dynamical equations. The Journal of Chemical Physics. 148: 241723. PMID 29960307 DOI: 10.1063/1.5018409 |
0.335 |
|
2018 |
Chen J, Chen J, Pinamonti G, Clementi C. Learning effective molecular models from experimental observables. Journal of Chemical Theory and Computation. PMID 29806937 DOI: 10.1021/Acs.Jctc.8B00187 |
0.472 |
|
2018 |
Litzinger F, Boninsegna L, Wu H, Nüske F, Patel R, Baraniuk R, Noé F, Clementi C. Rapid calculation of molecular kinetics using compressed sensing. Journal of Chemical Theory and Computation. PMID 29660273 DOI: 10.1021/Acs.Jctc.8B00089 |
0.397 |
|
2018 |
Boninsegna L, Banisch R, Clementi C. A Data-Driven Perspective on the Hierarchical Assembly of Molecular Structures. Journal of Chemical Theory and Computation. 14: 453-460. PMID 29207235 DOI: 10.1021/Acs.Jctc.7B00990 |
0.482 |
|
2017 |
Clementi C, Henkelman G. Preface: Special Topic on Reaction Pathways. The Journal of Chemical Physics. 147: 152401. PMID 29055311 DOI: 10.1063/1.5007080 |
0.308 |
|
2017 |
Olsson S, Wu H, Paul F, Clementi C, Noé F. Combining experimental and simulation data of molecular processes via augmented Markov models. Proceedings of the National Academy of Sciences of the United States of America. PMID 28716931 DOI: 10.1073/Pnas.1704803114 |
0.406 |
|
2017 |
Agarwal A, Clementi C, Delle Site L. Path integral-GC-AdResS simulation of a large hydrophobic solute in water: a tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space. Physical Chemistry Chemical Physics : Pccp. PMID 28484764 DOI: 10.1039/C7Cp01629H |
0.382 |
|
2017 |
Noé F, Clementi C. Collective variables for the study of long-time kinetics from molecular trajectories: theory and methods. Current Opinion in Structural Biology. 43: 141-147. PMID 28327454 DOI: 10.1016/J.Sbi.2017.02.006 |
0.376 |
|
2017 |
Nüske F, Wu H, Prinz J, Wehmeyer C, Clementi C, Noé F. Markov state models from short non-equilibrium simulations—Analysis and correction of estimation bias The Journal of Chemical Physics. 146: 094104. DOI: 10.1063/1.4976518 |
0.361 |
|
2016 |
Noé F, Banisch R, Clementi C. Commute maps: separating slowly-mixing molecular configurations for kinetic modeling. Journal of Chemical Theory and Computation. PMID 27696838 DOI: 10.1021/Acs.Jctc.6B00762 |
0.41 |
|
2015 |
Boninsegna L, Gobbo G, Noé F, Clementi C. Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps. Journal of Chemical Theory and Computation. 11: 5947-60. PMID 26580713 DOI: 10.1021/Acs.Jctc.5B00749 |
0.388 |
|
2015 |
Noé F, Clementi C. Kinetic distance and kinetic maps from molecular dynamics simulation. Journal of Chemical Theory and Computation. 11: 5002-11. PMID 26574285 DOI: 10.1021/Acs.Jctc.5B00553 |
0.471 |
|
2015 |
Cazade PA, Zheng W, Prada-Gracia D, Berezovska G, Rao F, Clementi C, Meuwly M. A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks. The Journal of Chemical Physics. 142: 025103. PMID 25591387 DOI: 10.1063/1.4904431 |
0.314 |
|
2014 |
A Rohrdanz M, Zheng W, Lambeth B, Vreede J, Clementi C. Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble. Plos Computational Biology. 10: e1003797. PMID 25356903 DOI: 10.1371/Journal.Pcbi.1003797 |
0.76 |
|
2014 |
Preto J, Clementi C. Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics. Physical Chemistry Chemical Physics : Pccp. 16: 19181-91. PMID 24955434 DOI: 10.1039/C3Cp54520B |
0.422 |
|
2014 |
A. Rohrdanz M, Zheng W, Lambeth B, Vreede J, Clementi C. Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble Plos Computational Biology. 10. DOI: 10.1371/journal.pcbi.1003797 |
0.745 |
|
2013 |
Zheng W, Vargiu AV, Vargiu AV, Rohrdanz MA, Carloni P, Clementi C. Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile. The Journal of Chemical Physics. 139: 145102. PMID 24116648 DOI: 10.1063/1.4824106 |
0.327 |
|
2013 |
Zheng W, Rohrdanz MA, Clementi C. Rapid exploration of configuration space with diffusion-map-directed molecular dynamics. The Journal of Physical Chemistry. B. 117: 12769-76. PMID 23865517 DOI: 10.1021/Jp401911H |
0.37 |
|
2013 |
Rohrdanz MA, Zheng W, Clementi C. Discovering mountain passes via torchlight: methods for the definition of reaction coordinates and pathways in complex macromolecular reactions. Annual Review of Physical Chemistry. 64: 295-316. PMID 23298245 DOI: 10.1146/Annurev-Physchem-040412-110006 |
0.315 |
|
2013 |
Rohrdanz MA, Zheng W, Lambeth B, Clementi C. Multiscale characterization of macromolecular dynamics: Application to photoacitve yellow protein Acm International Conference Proceeding Series. DOI: 10.1145/2484762.2484836 |
0.769 |
|
2012 |
Davtyan A, Schafer NP, Zheng W, Clementi C, Wolynes PG, Papoian GA. AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing. The Journal of Physical Chemistry. B. 116: 8494-503. PMID 22545654 DOI: 10.1021/Jp212541Y |
0.38 |
|
2011 |
Zheng W, Qi B, Rohrdanz MA, Caflisch A, Dinner AR, Clementi C. Delineation of folding pathways of a β-sheet miniprotein. The Journal of Physical Chemistry. B. 115: 13065-74. PMID 21942785 DOI: 10.1021/Jp2076935 |
0.422 |
|
2011 |
Ledbetter PJ, Clementi C. A new perspective on transition states: χ1 separatrix. The Journal of Chemical Physics. 135: 044116. PMID 21806099 DOI: 10.1063/1.3610957 |
0.324 |
|
2011 |
Zheng W, Rohrdanz MA, Maggioni M, Clementi C. Polymer reversal rate calculated via locally scaled diffusion map. The Journal of Chemical Physics. 134: 144109. PMID 21495744 DOI: 10.1063/1.3575245 |
0.376 |
|
2011 |
Rohrdanz MA, Zheng W, Maggioni M, Clementi C. Determination of reaction coordinates via locally scaled diffusion map. The Journal of Chemical Physics. 134: 124116. PMID 21456654 DOI: 10.1063/1.3569857 |
0.43 |
|
2010 |
Lambeth BP, Junghans C, Kremer K, Clementi C, Delle Site L. Communication: On the locality of hydrogen bond networks at hydrophobic interfaces. The Journal of Chemical Physics. 133: 221101. PMID 21171675 DOI: 10.1063/1.3522773 |
0.71 |
|
2010 |
Stamati H, Clementi C, Kavraki LE. Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides. Proteins. 78: 223-35. PMID 19731366 DOI: 10.1002/Prot.22526 |
0.455 |
|
2009 |
Hegler JA, Lätzer J, Shehu A, Clementi C, Wolynes PG. Restriction versus guidance in protein structure prediction. Proceedings of the National Academy of Sciences of the United States of America. 106: 15302-7. PMID 19706384 DOI: 10.1073/Pnas.0907002106 |
0.46 |
|
2009 |
Shehu A, Kavraki LE, Clementi C. Multiscale characterization of protein conformational ensembles. Proteins. 76: 837-51. PMID 19280604 DOI: 10.1002/Prot.22390 |
0.409 |
|
2009 |
Clementi C. Prediction of protein functional states by multi-resolution protein modeling Biophysical Journal. 96: 552a. DOI: 10.1016/J.Bpj.2008.12.2990 |
0.437 |
|
2008 |
Shehu A, Kavraki LE, Clementi C. Unfolding the fold of cyclic cysteine-rich peptides. Protein Science : a Publication of the Protein Society. 17: 482-93. PMID 18287281 DOI: 10.1110/Ps.073142708 |
0.383 |
|
2008 |
Matysiak S, Clementi C, Praprotnik M, Kremer K, Delle Site L. Modeling diffusive dynamics in adaptive resolution simulation of liquid water. The Journal of Chemical Physics. 128: 024503. PMID 18205455 DOI: 10.1063/1.2819486 |
0.697 |
|
2008 |
Clementi C. Coarse-grained models of protein folding: toy models or predictive tools? Current Opinion in Structural Biology. 18: 10-5. PMID 18160277 DOI: 10.1016/J.Sbi.2007.10.005 |
0.504 |
|
2008 |
Matysiak S, Clementi C. Mapping folding energy landscapes with theory and experiment. Archives of Biochemistry and Biophysics. 469: 29-33. PMID 17910943 DOI: 10.1016/J.Abb.2007.08.019 |
0.733 |
|
2007 |
Heath AP, Kavraki LE, Clementi C. From coarse-grain to all-atom: toward multiscale analysis of protein landscapes. Proteins. 68: 646-61. PMID 17523187 DOI: 10.1002/Prot.21371 |
0.455 |
|
2007 |
Mossa A, Clementi C. Supersymmetric Langevin equation to explore free-energy landscapes. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 75: 046707. PMID 17501016 DOI: 10.1103/Physreve.75.046707 |
0.349 |
|
2007 |
Plaku E, Stamati H, Clementi C, Kavraki LE. Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction. Proteins. 67: 897-907. PMID 17380507 DOI: 10.1002/Prot.21337 |
0.35 |
|
2007 |
Shehu A, Kavraki LE, Clementi C. On the characterization of protein native state ensembles. Biophysical Journal. 92: 1503-11. PMID 17158570 DOI: 10.1529/Biophysj.106.094409 |
0.512 |
|
2007 |
Praprotnik M, Matysiak S, Site LD, Kremer K, Clementi C. Adaptive resolution simulation of liquid water Journal of Physics: Condensed Matter. 19: 292201. DOI: 10.1088/0953-8984/19/29/292201 |
0.684 |
|
2007 |
Shehu A, Clementi C, Kavraki LE. Sampling conformation space to model equilibrium fluctuations in proteins Algorithmica (New York). 48: 303-327. DOI: 10.1007/S00453-007-0178-0 |
0.363 |
|
2006 |
Mossa A, Pettini M, Clementi C. Hamiltonian dynamics of homopolymer chain models. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 74: 041805. PMID 17155086 DOI: 10.1103/Physreve.74.041805 |
0.359 |
|
2006 |
Matysiak S, Clementi C. Minimalist protein model as a diagnostic tool for misfolding and aggregation. Journal of Molecular Biology. 363: 297-308. PMID 16959265 DOI: 10.1016/J.Jmb.2006.07.088 |
0.712 |
|
2006 |
Shehu A, Clementi C, Kavraki LE. Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations. Proteins. 65: 164-79. PMID 16917941 DOI: 10.1002/Prot.21060 |
0.462 |
|
2006 |
Das P, Moll M, Stamati H, Kavraki LE, Clementi C. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction. Proceedings of the National Academy of Sciences of the United States of America. 103: 9885-90. PMID 16785435 DOI: 10.1073/Pnas.0603553103 |
0.71 |
|
2006 |
Matysiak S, Montesi A, Pasquali M, Kolomeisky AB, Clementi C. Dynamics of polymer translocation through nanopores: theory meets experiment. Physical Review Letters. 96: 118103. PMID 16605877 DOI: 10.1103/Physrevlett.96.118103 |
0.658 |
|
2005 |
Wilson CJ, Das P, Clementi C, Matthews KS, Wittung-Stafshede P. The experimental folding landscape of monomeric lactose repressor, a large two-domain protein, involves two kinetic intermediates. Proceedings of the National Academy of Sciences of the United States of America. 102: 14563-8. PMID 16203983 DOI: 10.1073/Pnas.0505808102 |
0.695 |
|
2005 |
Das P, Wilson CJ, Fossati G, Wittung-Stafshede P, Matthews KS, Clementi C. Characterization of the folding landscape of monomeric lactose repressor: quantitative comparison of theory and experiment. Proceedings of the National Academy of Sciences of the United States of America. 102: 14569-74. PMID 16203982 DOI: 10.1073/Pnas.0505844102 |
0.726 |
|
2005 |
Das P, Matysiak S, Clementi C. Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes. Proceedings of the National Academy of Sciences of the United States of America. 102: 10141-6. PMID 16006532 DOI: 10.1073/Pnas.0409471102 |
0.786 |
|
2004 |
Matysiak S, Clementi C. Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: how far can a minimalist model go? Journal of Molecular Biology. 343: 235-48. PMID 15381433 DOI: 10.1016/J.Jmb.2004.08.006 |
0.727 |
|
2004 |
Chavez LL, Onuchic JN, Clementi C. Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates. Journal of the American Chemical Society. 126: 8426-32. PMID 15237999 DOI: 10.1021/Ja049510+ |
0.459 |
|
2004 |
Clementi C, Plotkin SS. The effects of nonnative interactions on protein folding rates: theory and simulation. Protein Science : a Publication of the Protein Society. 13: 1750-66. PMID 15215519 DOI: 10.1110/Ps.03580104 |
0.418 |
|
2003 |
Clementi C, GarcÃa AE, Onuchic JN. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L. Journal of Molecular Biology. 326: 933-54. PMID 12581651 DOI: 10.1016/S0022-2836(02)01379-7 |
0.48 |
|
2001 |
Clementi C, Jennings PA, Onuchic JN. Prediction of folding mechanism for circular-permuted proteins. Journal of Molecular Biology. 311: 879-90. PMID 11518537 DOI: 10.1006/Jmbi.2001.4871 |
0.49 |
|
2000 |
Cerruti-Sola M, Clementi C, Pettini M. Hamiltonian dynamics and geometry of phase transitions in classical XY models Physical Review E. 61: 5171-5190. PMID 11031563 DOI: 10.1103/Physreve.61.5171 |
0.327 |
|
2000 |
Clementi C, Jennings PA, Onuchic JN. How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta. Proceedings of the National Academy of Sciences of the United States of America. 97: 5871-6. PMID 10811910 DOI: 10.1073/Pnas.100547897 |
0.435 |
|
2000 |
Clementi C, Nymeyer H, Onuchic JN. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. Journal of Molecular Biology. 298: 937-53. PMID 10801360 DOI: 10.1006/Jmbi.2000.3693 |
0.496 |
|
2000 |
Clementi C, Vendruscolo M, Maritan A, Domany E. Folding Lennard-Jones proteins by a contact potential. Proteins. 37: 544-53. PMID 10651270 DOI: 10.1002/(Sici)1097-0134(19991201)37:4<544::Aid-Prot5>3.0.Co;2-7 |
0.412 |
|
1999 |
Clementi C, Carloni P, Maritan A. Protein design is a key factor for subunit–subunit association Proceedings of the National Academy of Sciences of the United States of America. 96: 9616-9621. PMID 10449742 DOI: 10.1073/Pnas.96.17.9616 |
0.369 |
|
1999 |
van Mourik J, Clementi C, Maritan A, Seno F, Banavar JR. Determination of interaction potentials of amino acids from native protein structures: Tests on simple lattice models The Journal of Chemical Physics. 110: 10123-10133. DOI: 10.1063/1.478885 |
0.439 |
|
1998 |
Clementi C, Maritan A, Banavar JR. Folding, Design, and Determination of Interaction Potentials Using Off-Lattice Dynamics of Model Heteropolymers Physical Review Letters. 81: 3287-3290. DOI: 10.1103/Physrevlett.81.3287 |
0.359 |
|
1998 |
Caiani L, Casetti L, Clementi C, Pettini G, Pettini M, Gatto R. Geometry of dynamics and phase transitions in classical latticeφ4theories Physical Review E. 57: 3886-3899. DOI: 10.1103/Physreve.57.3886 |
0.329 |
|
1997 |
Caiani L, Casetti L, Clementi C, Pettini M. Geometry of Dynamics, Lyapunov Exponents, and Phase Transitions Physical Review Letters. 79: 4361-4364. DOI: 10.1103/Physrevlett.79.4361 |
0.319 |
|
1996 |
Casetti L, Clementi C, Pettini M. Riemannian theory of Hamiltonian chaos and Lyapunov exponents. Physical Review E. 54: 5969-5984. PMID 9965813 DOI: 10.1103/Physreve.54.5969 |
0.324 |
|
Low-probability matches (unlikely to be authored by this person) |
2023 |
Zaporozhets I, Clementi C. Multibody Terms in Protein Coarse-Grained Models: A Top-Down Perspective. The Journal of Physical Chemistry. B. 127: 6920-6927. PMID 37499123 DOI: 10.1021/acs.jpcb.3c04493 |
0.299 |
|
2002 |
Clementi C, Pettini M. Celestial Mechanics and Dynamical Astronomy. 84: 263-281. DOI: 10.1023/A:1020345212438 |
0.294 |
|
2022 |
Mardt A, Hempel T, Clementi C, Noé F. Deep learning to decompose macromolecules into independent Markovian domains. Nature Communications. 13: 7101. PMID 36402768 DOI: 10.1038/s41467-022-34603-z |
0.29 |
|
2015 |
Boareto M, Jolly MK, Lu M, Onuchic JN, Clementi C, Ben-Jacob E. Jagged-Delta asymmetry in Notch signaling can give rise to a Sender/Receiver hybrid phenotype. Proceedings of the National Academy of Sciences of the United States of America. 112: E402-9. PMID 25605936 DOI: 10.1073/Pnas.1416287112 |
0.288 |
|
2018 |
Krylov A, Windus TL, Barnes T, Marin-Rimoldi E, Nash JA, Pritchard B, Smith DGA, Altarawy D, Saxe P, Clementi C, Crawford TD, Harrison RJ, Jha S, Pande VS, Head-Gordon T. Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science. The Journal of Chemical Physics. 149: 180901. PMID 30441927 DOI: 10.1063/1.5052551 |
0.286 |
|
2023 |
Arts M, Garcia Satorras V, Huang CW, Zügner D, Federici M, Clementi C, Noé F, Pinsler R, van den Berg R. Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics. Journal of Chemical Theory and Computation. 19: 6151-6159. PMID 37688551 DOI: 10.1021/acs.jctc.3c00702 |
0.282 |
|
2019 |
Abella JR, Antunes DA, Clementi C, Kavraki LE. APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations. Molecules (Basel, Switzerland). 24. PMID 30832312 DOI: 10.3390/Molecules24050881 |
0.281 |
|
2023 |
Yang W, Templeton C, Rosenberger D, Bittracher A, Nüske F, Noé F, Clementi C. Slicing and Dicing: Optimal Coarse-Grained Representation to Preserve Molecular Kinetics. Acs Central Science. 9: 186-196. PMID 36844497 DOI: 10.1021/acscentsci.2c01200 |
0.276 |
|
2021 |
Chen Y, Krämer A, Charron NE, Husic BE, Clementi C, Noé F. Machine learning implicit solvation for molecular dynamics. The Journal of Chemical Physics. 155: 084101. PMID 34470360 DOI: 10.1063/5.0059915 |
0.275 |
|
2015 |
Jolly MK, Boareto M, Lu M, Onuchic JN, Clementi C, Ben-Jacob E. Operating principles of Notch-Delta-Jagged module of cell-cell communication New Journal of Physics. 17. DOI: 10.1088/1367-2630/17/5/055021 |
0.271 |
|
2020 |
Hruska E, Balasubramanian V, Lee H, Jha S, Clementi C. Extensible and Scalable Adaptive Sampling on Supercomputers. Journal of Chemical Theory and Computation. PMID 33170696 DOI: 10.1021/acs.jctc.0c00991 |
0.262 |
|
2021 |
Wang J, Charron N, Husic B, Olsson S, Noé F, Clementi C. Multi-body effects in a coarse-grained protein force field. The Journal of Chemical Physics. 154: 164113. PMID 33940848 DOI: 10.1063/5.0041022 |
0.259 |
|
2020 |
Chen M, Chen X, Schafer NP, Clementi C, Komives EA, Ferreiro DU, Wolynes PG. Surveying biomolecular frustration at atomic resolution. Nature Communications. 11: 5944. PMID 33230150 DOI: 10.1038/s41467-020-19560-9 |
0.224 |
|
2013 |
Zheng W, Vargiu AV, Rohrdanz MA, Carloni P, Clementi C. Publisher's Note: “Molecular recognition of DNA by ligands: Roughness and complexity of the free energy profile” [J. Chem. Phys. 139, 145102 (2013)] The Journal of Chemical Physics. 139: 229901. DOI: 10.1063/1.4843495 |
0.214 |
|
2023 |
Meng X, Templeton C, Clementi C, Veit M. The role of an amphiphilic helix and transmembrane region in the efficient acylation of the M2 protein from influenza virus. Scientific Reports. 13: 18928. PMID 37919373 DOI: 10.1038/s41598-023-45945-z |
0.208 |
|
2022 |
Musil F, Zaporozhets I, Noé F, Clementi C, Kapil V. Quantum dynamics using path integral coarse-graining. The Journal of Chemical Physics. 157: 181102. PMID 36379765 DOI: 10.1063/5.0120386 |
0.205 |
|
2014 |
Sambasivan R, Zheng W, Burya SJ, Popp BV, Turro C, Clementi C, Ball ZT. A tripodal peptide ligand for asymmetric Rh(ii) catalysis highlights unique features of on-bead catalyst development Chemical Science. 5: 1401-1407. DOI: 10.1039/C3Sc53354A |
0.205 |
|
2023 |
Köhler J, Chen Y, Krämer A, Clementi C, Noé F. Flow-Matching: Efficient Coarse-Graining of Molecular Dynamics without Forces. Journal of Chemical Theory and Computation. PMID 36668906 DOI: 10.1021/acs.jctc.3c00016 |
0.205 |
|
2021 |
Doerr S, Majewski M, Pérez A, Krämer A, Clementi C, Noe F, Giorgino T, De Fabritiis G. TorchMD: A Deep Learning Framework for Molecular Simulations. Journal of Chemical Theory and Computation. PMID 33729795 DOI: 10.1021/acs.jctc.0c01343 |
0.204 |
|
2023 |
Krämer A, Durumeric AEP, Charron NE, Chen Y, Clementi C, Noé F. Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics. The Journal of Physical Chemistry Letters. 14: 3970-3979. PMID 37079800 DOI: 10.1021/acs.jpclett.3c00444 |
0.203 |
|
2021 |
Nüske F, Koltai P, Boninsegna L, Clementi C. Spectral Properties of Effective Dynamics from Conditional Expectations. Entropy (Basel, Switzerland). 23. PMID 33494443 DOI: 10.3390/e23020134 |
0.195 |
|
2021 |
Glielmo A, Husic BE, Rodriguez A, Clementi C, Noé F, Laio A. Unsupervised Learning Methods for Molecular Simulation Data. Chemical Reviews. PMID 33945269 DOI: 10.1021/acs.chemrev.0c01195 |
0.191 |
|
2020 |
Husic BE, Charron NE, Lemm D, Wang J, Pérez A, Majewski M, Krämer A, Chen Y, Olsson S, de Fabritiis G, Noé F, Clementi C. Coarse graining molecular dynamics with graph neural networks. The Journal of Chemical Physics. 153: 194101. PMID 33218238 DOI: 10.1063/5.0026133 |
0.187 |
|
2020 |
Wang J, Chmiela S, Müller KR, Noé F, Clementi C. Ensemble learning of coarse-grained molecular dynamics force fields with a kernel approach. The Journal of Chemical Physics. 152: 194106. PMID 33687259 DOI: 10.1063/5.0007276 |
0.167 |
|
2020 |
Abella JR, Antunes D, Jackson K, Lizée G, Clementi C, Kavraki LE. Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes. Proceedings of the National Academy of Sciences of the United States of America. PMID 33184174 DOI: 10.1073/pnas.2007246117 |
0.164 |
|
2022 |
Invernizzi M, Krämer A, Clementi C, Noé F. Skipping the Replica Exchange Ladder with Normalizing Flows. The Journal of Physical Chemistry Letters. 13: 11643-11649. PMID 36484770 DOI: 10.1021/acs.jpclett.2c03327 |
0.163 |
|
2023 |
Durumeric AEP, Charron NE, Templeton C, Musil F, Bonneau K, Pasos-Trejo AS, Chen Y, Kelkar A, Noé F, Clementi C. Machine learned coarse-grained protein force-fields: Are we there yet? Current Opinion in Structural Biology. 79: 102533. PMID 36731338 DOI: 10.1016/j.sbi.2023.102533 |
0.16 |
|
2011 |
Das P, Frewen TA, Kevrekidis IG, Clementi C. Think globally, move locally: Coarse graining of effective free energy surfaces Lecture Notes in Computational Science and Engineering. 75: 113-131. DOI: 10.1007/978-3-642-14941-2_6 |
0.14 |
|
2021 |
Clementi C. Fast track to structural biology. Nature Chemistry. 13: 1032-1034. PMID 34707232 DOI: 10.1038/s41557-021-00814-y |
0.117 |
|
2021 |
Lin X, George JT, Schafer NP, Chau KN, Birnbaum ME, Clementi C, Onuchic JN, Levine H. Rapid Assessment of T-Cell Receptor Specificity of the Immune Repertoire. Nature Computational Science. 1: 362-373. PMID 36090450 DOI: 10.1038/s43588-021-00076-1 |
0.103 |
|
2021 |
Ceriotti M, Clementi C, Anatole von Lilienfeld O. Machine learning meets chemical physics. The Journal of Chemical Physics. 154: 160401. PMID 33940847 DOI: 10.1063/5.0051418 |
0.081 |
|
2021 |
Ceriotti M, Clementi C, Anatole von Lilienfeld O. Introduction: Machine Learning at the Atomic Scale. Chemical Reviews. 121: 9719-9721. PMID 34428897 DOI: 10.1021/acs.chemrev.1c00598 |
0.073 |
|
2015 |
Cazade PA, Zheng W, Prada-Gracia D, Berezovska G, Rao F, Clementi C, Meuwly M. A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin i from transition networks Journal of Chemical Physics. 142. DOI: 10.1063/1.4904431 |
0.058 |
|
2006 |
Ogden J, Clementi C, Aylwin S. The impact of obesity surgery and the paradox of control: A qualitative study. Psychology & Health. 21: 273-93. PMID 21985121 DOI: 10.1080/14768320500129064 |
0.038 |
|
2011 |
Grandi S, Clementi C, Guidi J, Benassi M, Tossani E. Personality characteristics and psychological distress associated with primary exercise dependence: an exploratory study. Psychiatry Research. 189: 270-5. PMID 21459457 DOI: 10.1016/j.psychres.2011.02.025 |
0.034 |
|
2019 |
Gentilucci UV, Rosina F, Chessa L, Palitti VP, Picardi A, Barlattani M, Barlattani A, Feletti V, Musetto A, Zolfino T, russello m, Cannavo Mr, Cozzolongo R, Losito F, Garrucciu G, ... ... Clementi C, et al. FRI-067-Management of primary biliary cholangitis in the pre-obeticholic acid era, and the rate of non-response to ursodeoxycholic acid (UDCA), in a large real-world cohort of PBC patients in Italy: The CLEO-AIGO database Journal of Hepatology. 70: e415. DOI: 10.1016/S0618-8278(19)30817-5 |
0.03 |
|
2005 |
Ogden J, Clementi C, Aylwin S, Patel A. Exploring the impact of obesity surgery on patients' health status: a quantitative and qualitative study. Obesity Surgery. 15: 266-72. PMID 15802072 DOI: 10.1381/0960892053268291 |
0.026 |
|
2013 |
Guidi J, Clementi C, Grandi S. [Psychological distress and personality characteristics among individuals with primary exercise dependence]. Rivista Di Psichiatria. 48: 121-9. PMID 23748722 DOI: 10.1708/1272.14036 |
0.017 |
|
2017 |
Clementi C, Casu G, Gremigni P. An Abbreviated Version of the Mindful Eating Questionnaire. Journal of Nutrition Education and Behavior. 49: 352-356.e1. PMID 28391799 DOI: 10.1016/j.jneb.2017.01.016 |
0.01 |
|
Hide low-probability matches. |