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, 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 |
0.32 |
|
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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