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Cecilia Clementi - Publications

Affiliations: 
Rice University, Houston, TX 
Area:
General Biophysics
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81 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

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, García 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
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