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Cecilia Clementi - Publications

Affiliations: 
Rice University, Houston, TX 
Area:
General Biophysics
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43 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
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  0.36
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  0.36
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  0.36
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  0.36
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  0.44
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.44
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  0.36
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  0.32
2009 Shehu A, Kavraki LE, Clementi C. Multiscale characterization of protein conformational ensembles. Proteins. 76: 837-51. PMID 19280604 DOI: 10.1002/Prot.22390  0.32
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  0.32
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  1
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  1
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  0.36
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  0.36
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  0.32
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  0.32
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  1
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  0.32
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  0.92
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  0.32
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  0.32
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  0.32
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  1
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  1
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+  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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