| Year |
Citation |
Score |
| 2023 |
Costa MGS, Batista PR, Gomes A, Bastos LS, Louet M, Floquet N, Bisch PM, Perahia D. MDexciteR: Enhanced Sampling Molecular Dynamics by Excited Normal Modes or Principal Components Obtained from Experiments. Journal of Chemical Theory and Computation. PMID 36622950 DOI: 10.1021/acs.jctc.2c00599 |
0.333 |
|
| 2022 |
Kaynak BT, Krieger JM, Dudas B, Dahmani ZL, Costa MGS, Balog E, Scott AL, Doruker P, Perahia D, Bahar I. Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods. Frontiers in Molecular Biosciences. 9: 832847. PMID 35187088 DOI: 10.3389/fmolb.2022.832847 |
0.649 |
|
| 2020 |
Krieger JM, Doruker P, Scott AL, Perahia D, Bahar I. Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods. Current Opinion in Structural Biology. 64: 34-41. PMID 32622329 DOI: 10.1016/J.Sbi.2020.05.013 |
0.64 |
|
| 2020 |
Resende-Lara PT, Perahia D, Scott AL, Braz ASK. Unveiling functional motions based on point mutations in biased signaling systems: A normal mode study on nerve growth factor bound to TrkA. Plos One. 15: e0231542. PMID 32497034 DOI: 10.1371/journal.pone.0231542 |
0.542 |
|
| 2020 |
Costa MGS, Fagnen C, Vénien-Bryan C, Perahia D. A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit). Journal of Chemical Information and Modeling. PMID 31944765 DOI: 10.1021/acs.jcim.9b01148 |
0.313 |
|
| 2018 |
Pantaleão SQ, Philot EA, de Resende-Lara PT, Lima AN, Perahia D, Miteva MA, Scott AL, Honorio KM. Structural Dynamics of DPP-4 and Its Influence on the Projection of Bioactive Ligands. Molecules (Basel, Switzerland). 23. PMID 29473857 DOI: 10.3390/Molecules23020490 |
0.578 |
|
| 2015 |
Moroy G, Sperandio O, Rielland S, Khemka S, Druart K, Goyal D, Perahia D, Miteva MA. Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis. Future Medicinal Chemistry. 7: 2317-31. PMID 26599419 DOI: 10.4155/fmc.15.150 |
0.303 |
|
| 2015 |
Costa MG, Batista PR, Bisch PM, Perahia D. Exploring Free Energy Landscapes of Large Conformational Changes: Molecular Dynamics with Excited Normal Modes. Journal of Chemical Theory and Computation. 11: 2755-67. PMID 26575568 DOI: 10.1021/acs.jctc.5b00003 |
0.361 |
|
| 2011 |
Louet M, Perahia D, Martinez J, Floquet N. A concerted mechanism for opening the GDP binding pocket and release of the nucleotide in hetero-trimeric G-proteins. Journal of Molecular Biology. 411: 298-312. PMID 21663745 DOI: 10.1016/J.Jmb.2011.05.034 |
0.344 |
|
| 2011 |
Balog E, Perahia D, Smith JC, Merzel F. Vibrational softening of a protein on ligand binding. The Journal of Physical Chemistry. B. 115: 6811-7. PMID 21553905 DOI: 10.1021/Jp108493G |
0.469 |
|
| 2010 |
Batista PR, Robert CH, Maréchal JD, Hamida-Rebaï MB, Pascutti PG, Bisch PM, Perahia D. Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis--application to the HIV-1 protease. Physical Chemistry Chemical Physics : Pccp. 12: 2850-9. PMID 20449375 DOI: 10.1039/b919148h |
0.356 |
|
| 2010 |
Levy RM, Perahia D, Karplus M. Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior. Proceedings of the National Academy of Sciences of the United States of America. 79: 1346-50. PMID 16593164 DOI: 10.1073/Pnas.79.4.1346 |
0.576 |
|
| 2006 |
Balog E, Smith JC, Perahia D. Conformational heterogeneity and low-frequency vibrational modes of proteins. Physical Chemistry Chemical Physics : Pccp. 8: 5543-8. PMID 17136269 DOI: 10.1039/B610075A |
0.497 |
|
| 2004 |
Robert CH, Cherfils J, Mouawad L, Perahia D. Integrating three views of Arf1 activation dynamics. Journal of Molecular Biology. 337: 969-83. PMID 15033364 DOI: 10.1016/J.Jmb.2004.01.052 |
0.347 |
|
| 1999 |
Thomas A, Hinsen K, Field MJ, Perahia D. Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study. Proteins. 34: 96-112. PMID 10336386 DOI: 10.1002/(Sici)1097-0134(19990101)34:1<96::Aid-Prot8>3.0.Co;2-0 |
0.617 |
|
| 1998 |
Yon JM, Perahia D, Ghélis C. Conformational dynamics and enzyme activity. Biochimie. 80: 33-42. PMID 9587660 DOI: 10.1016/S0300-9084(98)80054-0 |
0.359 |
|
| 1997 |
Simonson T, Perahia D. Polar fluctuations in proteins: molecular-dynamic studies of cytochrome c in aqueous solution. Faraday Discussions. 71-90. PMID 9136636 DOI: 10.1039/Fd9960300071 |
0.422 |
|
| 1996 |
Thomas A, Field MJ, Perahia D. Analysis of the low-frequency normal modes of the R state of aspartate transcarbamylase and a comparison with the T state modes. Journal of Molecular Biology. 261: 490-506. PMID 8780788 DOI: 10.1006/Jmbi.1996.0478 |
0.557 |
|
| 1996 |
Thomas A, Field MJ, Mouawad L, Perahia D. Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase. Journal of Molecular Biology. 257: 1070-87. PMID 8632469 DOI: 10.1006/Jmbi.1996.0224 |
0.594 |
|
| 1996 |
Mouawad L, Perahia D. Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures. Journal of Molecular Biology. 258: 393-410. PMID 8627633 DOI: 10.1006/Jmbi.1996.0257 |
0.333 |
|
| 1995 |
Simonson T, Perahia D. Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution. Proceedings of the National Academy of Sciences of the United States of America. 92: 1082-6. PMID 7862638 DOI: 10.1073/Pnas.92.4.1082 |
0.354 |
|
| 1995 |
Perahia D, Mouawad L. Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin. Computers & Chemistry. 19: 241-6. PMID 7551557 DOI: 10.1016/0097-8485(95)00011-G |
0.404 |
|
| 1995 |
Simonson T, Perahia D. Microscopic Dielectric Properties of Cytochrome c from Molecular Dynamics Simulations in Aqueous Solution Journal of the American Chemical Society. 117: 7987-8000. DOI: 10.1021/Ja00135A018 |
0.306 |
|
| 1995 |
Simonson T, Perahia D. Dielectric properties of proteins from simulations: tools and techniques Computer Physics Communications. 91: 291-303. DOI: 10.1016/0010-4655(95)00054-J |
0.402 |
|
| 1994 |
Faure P, Micu A, Pérahia D, Doucet J, Smith JC, Benoit JP. Correlated intramolecular motions and diffuse x-ray scattering in lysozyme Nature Structural Biology. 1: 124-128. PMID 7656016 DOI: 10.1038/Nsb0294-124 |
0.417 |
|
| 1993 |
Mouawad L, Perahia D. Diagonalization in a mixed basis: A method to compute low-frequency normal modes for large macromolecules Biopolymers. 33: 599-611. DOI: 10.1002/Bip.360330409 |
0.382 |
|
| 1992 |
Simonson T, Perahia D. Normal modes of symmetric protein assemblies. Application to the tobacco mosaic virus protein disk. Biophysical Journal. 61: 410-27. PMID 1547329 DOI: 10.1016/S0006-3495(92)81847-7 |
0.425 |
|
| 1991 |
Yon JM, Desmadril M, Betton JM, Minard P, Ballery N, Missiakas D, Gaillard-Miran S, Perahia D, Mouawad L. Flexibility and folding of phosphoglycerate kinase. Biochimie. 72: 417-29. PMID 2124145 DOI: 10.1016/0300-9084(90)90066-P |
0.318 |
|
| 1991 |
Mouawad L, Desmadril M, Perahia D, Yon JM, Brochon JC. The effects of ligands on the conformation of phosphoglycerate kinase: fluorescence anisotropy decay and theoretical interpretation. Biopolymers. 30: 1151-60. PMID 2085655 DOI: 10.1002/Bip.360301302 |
0.367 |
|
| 1991 |
Simonson T, Perahia D, Bricogne G. Intramolecular dielectric screening in proteins. Journal of Molecular Biology. 218: 859-86. PMID 2023253 DOI: 10.1016/0022-2836(91)90273-9 |
0.371 |
|
| 1991 |
Simonson T, Perahia D, Brünger AT. Microscopic theory of the dielectric properties of proteins. Biophysical Journal. 59: 670-90. PMID 1646659 DOI: 10.1016/S0006-3495(91)82282-2 |
0.333 |
|
| 1991 |
Simonson T, Perahia D, Bricogne G, Brünger A. Dielectric properties of proteins : microscopic and macroscopic theory Journal De Chimie Physique. 88: 2701-2708. DOI: 10.1051/Jcp/1991882701 |
0.487 |
|
| 1990 |
Perahia D, Levy RM, Karplus M. Motions of an ?-helical polypeptide: Comparison of molecular and harmonic dynamics Biopolymers. 29: 645-677. DOI: 10.1002/Bip.360290402 |
0.61 |
|
| 1984 |
Levy RM, Karplus M, Kushick J, Perahia D. Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an α-helix Macromolecules. 17: 1370-1374. DOI: 10.1021/Ma00137A013 |
0.564 |
|
| 1979 |
Colonna-Cesari F, Perahia D, Karplus M, Eklund H, Brädén CI, Tapia O. Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode. Journal of Biological Chemistry. 261: 15273-15280. DOI: 10.2210/Pdb5Adh/Pdb |
0.488 |
|
| 1972 |
Pullman B, Perahia D, Saran A. Molecular orbital calculations on the conformation of nucleic acids and their constituents. 3. Backbone structure of di- and polynucleotides. Biochimica Et Biophysica Acta. 269: 1-14. PMID 5026319 DOI: 10.1016/0005-2787(72)90068-8 |
0.336 |
|
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