| Year |
Citation |
Score |
| 2023 |
Case DA, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VWD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, ... ... Roitberg A, et al. AmberTools. Journal of Chemical Information and Modeling. 63: 6183-6191. PMID 37805934 DOI: 10.1021/acs.jcim.3c01153 |
0.709 |
|
| 2022 |
Tracy DA, Fernandez-Alberti S, Tretiak S, Roitberg AE. Adiabatic Excited-State Molecular Dynamics with an Explicit Solvent: NEXMD-SANDER Implementation. Journal of Chemical Theory and Computation. PMID 36044726 DOI: 10.1021/acs.jctc.2c00561 |
0.302 |
|
| 2020 |
Malone W, Nebgen B, White A, Zhang Y, Song H, Bjorgaard JA, Sifain AE, Rodriguez-Hernandez B, Freixas VM, Fernandez-Alberti S, Roitberg AE, Nelson TR, Tretiak S. NEXMD Software Package for Non-adiabatic Excited State Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 32635739 DOI: 10.1021/Acs.Jctc.0C00248 |
0.403 |
|
| 2020 |
Devereux C, Smith JS, Davis KK, Barros K, Zubatyuk R, Isayev O, Roitberg AE. Extending the applicability of the ANI deep learning molecular potential to Sulfur and Halogens. Journal of Chemical Theory and Computation. PMID 32543858 DOI: 10.1021/Acs.Jctc.0C00121 |
0.312 |
|
| 2020 |
Gupta PL, Roitberg AE. Rationalizing the pH-Activity Response of Glycinamide Ribonucleotide Transformylase Through Computational Methods. The Journal of Physical Chemistry. B. PMID 32364730 DOI: 10.1021/Acs.Jpcb.0C03743 |
0.366 |
|
| 2020 |
Smith JS, Zubatyuk R, Nebgen B, Lubbers N, Barros K, Roitberg AE, Isayev O, Tretiak S. The ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for molecules. Scientific Data. 7: 134. PMID 32358545 DOI: 10.1038/S41597-020-0473-Z |
0.304 |
|
| 2020 |
Nelson TR, White AJ, Bjorgaard JA, Sifain AE, Zhang Y, Nebgen B, Fernandez-Alberti S, Mozyrsky D, Roitberg AE, Tretiak S. Non-adiabatic Excited-State Molecular Dynamics: Theory and Applications for Modeling Photophysics in Extended Molecular Materials. Chemical Reviews. PMID 32040312 DOI: 10.1021/Acs.Chemrev.9B00447 |
0.392 |
|
| 2020 |
Cruzeiro VWD, Feliciano GT, Roitberg AE. Exploring coupled redox and pH processes with a force field-based approach: applications to five different systems. Journal of the American Chemical Society. PMID 32011132 DOI: 10.1021/Jacs.9B11433 |
0.37 |
|
| 2019 |
Rodas JM, Galindo JF, Roitberg AE, Reyes A. The any particle molecular orbital/molecular mechanics approach. Journal of Molecular Modeling. 25: 316. PMID 31529219 DOI: 10.1007/S00894-019-4153-X |
0.328 |
|
| 2019 |
González-Lebrero RM, Defelipe L, Modenutti C, Roitberg AE, Batastini NA, Noguera ME, Santos J, Roman EA. Folding and Dynamics Are Strongly pH-Dependent in a Psychrophile Frataxin. The Journal of Physical Chemistry. B. PMID 31407901 DOI: 10.1021/Acs.Jpcb.9B05960 |
0.385 |
|
| 2019 |
Sarkar A, Gupta PL, Roitberg AE. pH-Dependent Conformational Changes Due to Ionizable Residues in a Hydrophobic Protein Interior: The Study of L25K and L125K Variants of SNase. The Journal of Physical Chemistry. B. PMID 31260304 DOI: 10.1021/Acs.Jpcb.9B03816 |
0.345 |
|
| 2019 |
Cruzeiro VWD, Roitberg AE. Multidimensional Replica Exchange simulations for Efficient constant pH and Redox Potential Molecular Dynamics. Journal of Chemical Theory and Computation. PMID 30615455 DOI: 10.1021/Acs.Jctc.8B00935 |
0.385 |
|
| 2019 |
Sarkar A, Roitberg AE. pH-Dependent Properties of Ionizable Residues in the Hydrophobic Interior of a Protein Biophysical Journal. 116: 476a. DOI: 10.1016/J.Bpj.2018.11.2570 |
0.323 |
|
| 2018 |
Ondarse-Alvarez D, Oldani N, Roitberg AE, Kleiman V, Tretiak S, Fernandez-Alberti S. Energy transfer and spatial scrambling of an exciton in a conjugated dendrimer. Physical Chemistry Chemical Physics : Pccp. 20: 29648-29660. PMID 30465570 DOI: 10.1039/C8Cp05852K |
0.348 |
|
| 2018 |
Lee TS, Cerutti DS, Mermelstein D, Lin C, LeGrand S, Giese TJ, Roitberg AE, Case DA, Walker RC, York DM. GPU-accelerated molecular dynamics and free energy methods in Amber18: performance enhancements and new features. Journal of Chemical Information and Modeling. PMID 30199633 DOI: 10.1021/Acs.Jcim.8B00462 |
0.39 |
|
| 2018 |
Cruzeiro VWD, Amaral MS, Roitberg AE. Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation. The Journal of Chemical Physics. 149: 072338. PMID 30134669 DOI: 10.1063/1.5027379 |
0.378 |
|
| 2018 |
Nebgen B, Lubbers N, Smith JS, Sifain AE, Lokhov A, Isayev O, Roitberg AE, Barros K, Tretiak S. Transferable Dynamic Molecular Charge Assignment Using Deep Neural Networks. Journal of Chemical Theory and Computation. PMID 30064217 DOI: 10.1021/Acs.Jctc.8B00524 |
0.349 |
|
| 2018 |
Chouinard CD, Cruzeiro VWD, Kemperman RHJ, Oranzi NR, Roitberg AE, Yost RA. Cation-Dependent Conformations in 25-Hydroxyvitamin D3-Cation Adducts Measured by Ion Mobility-Mass Spectrometry and Theoretical Modeling. International Journal of Mass Spectrometry. 432: 1-8. PMID 30034270 DOI: 10.1016/J.Ijms.2018.05.013 |
0.329 |
|
| 2018 |
Nelson TR, Ondarse-Alvarez D, Oldani N, Rodriguez-Hernandez B, Alfonso-Hernandez L, Galindo JF, Kleiman VD, Fernandez-Alberti S, Roitberg AE, Tretiak S. Coherent exciton-vibrational dynamics and energy transfer in conjugated organics. Nature Communications. 9: 2316. PMID 29899334 DOI: 10.1038/S41467-018-04694-8 |
0.381 |
|
| 2018 |
Sifain AE, Bjorgaard JA, Nelson TR, Nebgen BT, White AJ, Gifford BJ, Gao DW, Prezhdo OV, Fernandez-Alberti S, Roitberg AE, Tretiak S. Photoexcited Nonadiabatic Dynamics of Solvated Push-Pull π-Conjugated Oligomers with the NEXMD Software. Journal of Chemical Theory and Computation. PMID 29874465 DOI: 10.1021/Acs.Jctc.8B00103 |
0.378 |
|
| 2018 |
Liu J, Swails J, Zhang JZH, He X, Roitberg AE. A Coupled Ionization-Conformational Equilibrium Is Required To Understand The Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease. Journal of the American Chemical Society. PMID 29308643 DOI: 10.1021/Jacs.7B08569 |
0.767 |
|
| 2017 |
Smith JS, Isayev O, Roitberg AE. ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules. Scientific Data. 4: 170193. PMID 29257127 DOI: 10.1038/Sdata.2017.193 |
0.331 |
|
| 2017 |
Nelson TR, Fernandez-Alberti S, Roitberg AE, Tretiak S. Electronic Delocalization, Vibrational Dynamics and Energy Transfer in Organic Chromophores. The Journal of Physical Chemistry Letters. PMID 28603994 DOI: 10.1021/Acs.Jpclett.7B00790 |
0.339 |
|
| 2017 |
Smith JS, Isayev O, Roitberg AE. ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost. Chemical Science. 8: 3192-3203. PMID 28507695 DOI: 10.1039/C6Sc05720A |
0.311 |
|
| 2017 |
Chouinard CD, Cruzeiro VWD, Beekman CR, Roitberg AE, Yost RA. Investigating Differences in Gas-Phase Conformations of 25-Hydroxyvitamin D3 Sodiated Epimers using Ion Mobility-Mass Spectrometry and Theoretical Modeling. Journal of the American Society For Mass Spectrometry. PMID 28417307 DOI: 10.1007/S13361-017-1673-4 |
0.309 |
|
| 2016 |
Ondarse-Alvarez D, Kömürlü S, Roitberg AE, Pierdominici-Sottile G, Tretiak S, Fernandez-Alberti S, Kleiman VD. Ultrafast electronic energy relaxation in a conjugated dendrimer leading to inter-branch energy redistribution. Physical Chemistry Chemical Physics : Pccp. 18: 25080-25089. PMID 27711661 DOI: 10.1039/C6Cp04448D |
0.369 |
|
| 2016 |
Ramírez CL, Martí MA, Roitberg AE. Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics. Methods in Enzymology. 578: 123-43. PMID 27497165 DOI: 10.1016/Bs.Mie.2016.05.029 |
0.373 |
|
| 2016 |
Ithuralde RE, Roitberg AE, Turjanski AG. Structured and Unstructured binding of an Intrinsically Disordered Protein as revealed by atomistic simulations. Journal of the American Chemical Society. PMID 27348048 DOI: 10.1021/Jacs.6B02016 |
0.372 |
|
| 2016 |
Ramirez CL, Petruk A, Bringas M, Estrin DA, Roitberg AE, Marti MA, Capece L. Coarse-grained simulations of heme proteins: validation and study of large conformational transitions. Journal of Chemical Theory and Computation. PMID 27267322 DOI: 10.1021/Acs.Jctc.6B00278 |
0.375 |
|
| 2016 |
Alvarez L, Lewis Ballester A, Roitberg AE, Estrin DA, Yeh SR, Marti MA, Capece L. Structural study of a flexible active site loop in human indoleamine 2,3-dioxygenase and its functional implications. Biochemistry. PMID 27112409 DOI: 10.1021/Acs.Biochem.6B00077 |
0.373 |
|
| 2015 |
Hopkins CW, Le Grand S, Walker RC, Roitberg AE. Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning. Journal of Chemical Theory and Computation. 11: 1864-74. PMID 26574392 DOI: 10.1021/Ct5010406 |
0.331 |
|
| 2015 |
Galindo JF, Atas E, Altan A, Kuroda DG, Fernandez-Alberti S, Tretiak S, Roitberg AE, Kleiman VD. Correction to "Dynamics of Energy Transfer in a Conjugated Dendrimer Driven by Ultrafast Localization of Excitations". Journal of the American Chemical Society. 137: 14229. PMID 26509965 DOI: 10.1021/Jacs.5B09791 |
0.324 |
|
| 2015 |
Di Russo NV, Condurso HL, Li K, Bruner SD, Roitberg AE. Oxygen diffusion pathways in a cofactor-independent dioxygenase. Chemical Science (Royal Society of Chemistry : 2010). 6: 6341-6348. PMID 26508997 DOI: 10.1039/C5Sc01638J |
0.302 |
|
| 2015 |
Grosso M, Kalstein A, Parisi G, Roitberg AE, Fernandez-Alberti S. On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein. The Journal of Chemical Physics. 142: 245101. PMID 26133456 DOI: 10.1063/1.4922925 |
0.389 |
|
| 2015 |
Galindo JF, Atas E, Altan A, Kuroda DG, Fernandez-Alberti S, Tretiak S, Roitberg AE, Kleiman V. DYNAMICS OF ENERGY TRANSFER IN A CONJUGATED DENDRIMER DRIVEN BY ULTRAFAST LOCALIZATION OF EXCITATIONS. Journal of the American Chemical Society. PMID 26122872 DOI: 10.1021/Jacs.5B04075 |
0.335 |
|
| 2015 |
Alves CN, Silva JR, Roitberg AE. Insights into the mechanism of oxidation of dihydroorotate to orotate catalysed by human class 2 dihydroorotate dehydrogenase: a QM/MM free energy study. Physical Chemistry Chemical Physics : Pccp. PMID 26087682 DOI: 10.1039/C5Cp02016F |
0.334 |
|
| 2015 |
Dissanayake T, Swails JM, Harris ME, Roitberg AE, York DM. Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations. Biochemistry. 54: 1307-13. PMID 25615525 DOI: 10.1021/Bi5012833 |
0.749 |
|
| 2015 |
Silva JR, Roitberg AE, Alves CN. A QM/MM free energy study of the oxidation mechanism of dihydroorotate dehydrogenase (class 1A) from Lactococcus lactis. The Journal of Physical Chemistry. B. 119: 1468-73. PMID 25564307 DOI: 10.1021/Jp512860R |
0.347 |
|
| 2014 |
Ramírez CL, Zeida A, Jara GE, Roitberg AE, Martí MA. Improving Efficiency in SMD Simulations Through a Hybrid Differential Relaxation Algorithm. Journal of Chemical Theory and Computation. 10: 4609-17. PMID 26588154 DOI: 10.1021/Ct500672D |
0.345 |
|
| 2014 |
McGee TD, Edwards J, Roitberg AE. pH-REMD simulations indicate that the catalytic aspartates of HIV-1 protease exist primarily in a monoprotonated state. The Journal of Physical Chemistry. B. 118: 12577-85. PMID 25340507 DOI: 10.1021/Jp504011C |
0.363 |
|
| 2014 |
Di Russo NV, Martí MA, Roitberg AE. Underlying thermodynamics of pH-dependent allostery. The Journal of Physical Chemistry. B. 118: 12818-26. PMID 25318010 DOI: 10.1021/Jp507971V |
0.36 |
|
| 2014 |
Silva JR, Roitberg AE, Alves CN. Catalytic mechanism of L,D-transpeptidase 2 from Mycobacterium tuberculosis described by a computational approach: insights for the design of new antibiotics drugs. Journal of Chemical Information and Modeling. 54: 2402-10. PMID 25149147 DOI: 10.1021/Ci5003069 |
0.305 |
|
| 2014 |
Hopkins CW, Roitberg AE. Fitting of dihedral terms in classical force fields as an analytic linear least-squares problem. Journal of Chemical Information and Modeling. 54: 1978-86. PMID 24960267 DOI: 10.1021/Ci500112W |
0.333 |
|
| 2014 |
Bueren-Calabuig JA, Pierdominici-Sottile G, Roitberg AE. Unraveling the differences of the hydrolytic activity of Trypanosoma cruzi trans-sialidase and Trypanosoma rangeli sialidase: a quantum mechanics-molecular mechanics modeling study. The Journal of Physical Chemistry. B. 118: 5807-16. PMID 24814976 DOI: 10.1021/Jp412294R |
0.341 |
|
| 2014 |
Swails JM, York DM, Roitberg AE. Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation. Journal of Chemical Theory and Computation. 10: 1341-1352. PMID 24803862 DOI: 10.1021/Ct401042B |
0.77 |
|
| 2014 |
Nelson T, Fernandez-Alberti S, Roitberg AE, Tretiak S. Nonadiabatic excited-state molecular dynamics: modeling photophysics in organic conjugated materials. Accounts of Chemical Research. 47: 1155-64. PMID 24673100 DOI: 10.1021/Ar400263P |
0.399 |
|
| 2014 |
Bergonzo C, Henriksen NM, Roe DR, Swails JM, Roitberg AE, Cheatham TE. Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide. Journal of Chemical Theory and Computation. 10: 492-499. PMID 24453949 DOI: 10.1021/Ct400862K |
0.743 |
|
| 2013 |
Liang S, Roitberg AE. AM1 Specific Reaction Parameters for Reactions of Hydroxide Ion with Halomethanes in Complex Environments: Development and Testing. Journal of Chemical Theory and Computation. 9: 4470-80. PMID 26589165 DOI: 10.1021/Ct400471M |
0.308 |
|
| 2013 |
Sabri Dashti D, Roitberg AE. Optimization of Umbrella Sampling Replica Exchange Molecular Dynamics by Replica Positioning. Journal of Chemical Theory and Computation. 9: 4692-9. PMID 26583388 DOI: 10.1021/Ct400366H |
0.343 |
|
| 2013 |
Miller BR, Roitberg AE. Trypanosoma cruzi trans-sialidase as a drug target against Chagas disease (American trypanosomiasis). Future Medicinal Chemistry. 5: 1889-900. PMID 24144418 DOI: 10.4155/Fmc.13.129 |
0.683 |
|
| 2013 |
Miller BR, Roitberg AE. Design of e-pharmacophore models using compound fragments for the trans-sialidase of Trypanosoma cruzi: screening for novel inhibitor scaffolds. Journal of Molecular Graphics & Modelling. 45: 84-97. PMID 24012872 DOI: 10.1016/J.Jmgm.2013.08.009 |
0.695 |
|
| 2013 |
Nelson T, Fernandez-Alberti S, Roitberg AE, Tretiak S. Nonadiabatic excited-state molecular dynamics: treatment of electronic decoherence. The Journal of Chemical Physics. 138: 224111. PMID 23781787 DOI: 10.1063/1.4809568 |
0.343 |
|
| 2013 |
Nelson T, Fernandez-Alberti S, Roitberg AE, Tretiak S. Conformational disorder in energy transfer: beyond Förster theory. Physical Chemistry Chemical Physics : Pccp. 15: 9245-56. PMID 23657784 DOI: 10.1039/C3Cp50857A |
0.354 |
|
| 2013 |
Castro MA, Roitberg AE, Cukiernik FD. Simulation of mesogenic diruthenium tetracarboxylates: Development of a force field for coordination polymers of the MMX type. Journal of Computational Chemistry. 34: 1283-90. PMID 23436725 DOI: 10.1002/Jcc.23254 |
0.313 |
|
| 2013 |
Boechi L, Arrar M, Martà MA, Olson JS, Roitberg AE, Estrin DA. Hydrophobic effect drives oxygen uptake in myoglobin via histidine E7. The Journal of Biological Chemistry. 288: 6754-62. PMID 23297402 DOI: 10.1074/Jbc.M112.426056 |
0.316 |
|
| 2013 |
Galindo JF, Fernandez-Alberti S, Roitberg AE. Electronic excited state specific IR spectra for phenylene ethynylene dendrimer building blocks Journal of Physical Chemistry C. 117: 26517-26528. DOI: 10.1021/Jp4102652 |
0.352 |
|
| 2013 |
Nelson T, Fernandez-Alberti S, Roitberg AE, Tretiak S. Artifacts due to trivial unavoided crossings in the modeling of photoinduced energy transfer dynamics in extended conjugated molecules Chemical Physics Letters. 590: 208-213. DOI: 10.1016/J.Cplett.2013.10.052 |
0.371 |
|
| 2012 |
Miller BR, McGee TD, Swails JM, Homeyer N, Gohlke H, Roitberg AE. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. Journal of Chemical Theory and Computation. 8: 3314-3321. PMID 26605738 DOI: 10.1021/Ct300418H |
0.784 |
|
| 2012 |
Swails JM, Roitberg AE. Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics. Journal of Chemical Theory and Computation. 8: 4393-4404. PMID 26605601 DOI: 10.1021/Ct300512H |
0.757 |
|
| 2012 |
Fernandez-Alberti S, Roitberg AE, Kleiman VD, Nelson T, Tretiak S. Shishiodoshi unidirectional energy transfer mechanism in phenylene ethynylene dendrimers. The Journal of Chemical Physics. 137: 22A526. PMID 23249063 DOI: 10.1063/1.4745835 |
0.341 |
|
| 2012 |
Di Russo NV, Estrin DA, Martà MA, Roitberg AE. pH-Dependent conformational changes in proteins and their effect on experimental pK(a)s: the case of Nitrophorin 4. Plos Computational Biology. 8: e1002761. PMID 23133364 DOI: 10.1371/Journal.Pcbi.1002761 |
0.397 |
|
| 2012 |
Soler MA, Roitberg AE, Nelson T, Tretiak S, Fernandez-Alberti S. Analysis of state-specific vibrations coupled to the unidirectional energy transfer in conjugated dendrimers. The Journal of Physical Chemistry. A. 116: 9802-10. PMID 22985079 DOI: 10.1021/Jp301293E |
0.303 |
|
| 2012 |
Fernandez-Alberti S, Roitberg AE, Nelson T, Tretiak S. Identification of unavoided crossings in nonadiabatic photoexcited dynamics involving multiple electronic states in polyatomic conjugated molecules. The Journal of Chemical Physics. 137: 014512. PMID 22779670 DOI: 10.1063/1.4732536 |
0.369 |
|
| 2012 |
Sabri Dashti D, Meng Y, Roitberg AE. pH-replica exchange molecular dynamics in proteins using a discrete protonation method. The Journal of Physical Chemistry. B. 116: 8805-11. PMID 22694266 DOI: 10.1021/Jp303385X |
0.721 |
|
| 2012 |
Roberts BP, Miller BR, Roitberg AE, Merz KM. Wide-open flaps are key to urease activity. Journal of the American Chemical Society. 134: 9934-7. PMID 22670767 DOI: 10.1021/Ja3043239 |
0.715 |
|
| 2012 |
Roberts BP, Seabra GM, Roitberg AE, Merz KM, Deumens E, Torras J, Trickey SB. Comment on "A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation". Journal of Computational Chemistry. 33: 1643-4. PMID 22570199 DOI: 10.1002/Jcc.23003 |
0.317 |
|
| 2012 |
Nelson T, Fernandez-Alberti S, Chernyak V, Roitberg AE, Tretiak S. Nonadiabatic excited-state molecular dynamics: numerical tests of convergence and parameters. The Journal of Chemical Physics. 136: 054108. PMID 22320726 DOI: 10.1063/1.3680565 |
0.402 |
|
| 2012 |
Swails JM, Roitberg AE. Enhancing conformation and protonation state sampling of hen egg white lysozyme using pH replica exchange molecular dynamics Journal of Chemical Theory and Computation. 8: 4393-4404. DOI: 10.1021/ct300512h |
0.743 |
|
| 2012 |
Miller BR, McGee TD, Swails JM, Homeyer N, Gohlke H, Roitberg AE. MMPBSA.py: An efficient program for end-state free energy calculations Journal of Chemical Theory and Computation. 8: 3314-3321. DOI: 10.1021/ct300418h |
0.767 |
|
| 2011 |
Meng Y, Dashti DS, Roitberg AE. Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations. Journal of Chemical Theory and Computation. 7: 2721-2727. PMID 22125475 DOI: 10.1021/Ct200153U |
0.724 |
|
| 2011 |
Pierdominici-Sottile G, Horenstein NA, Roitberg AE. Free energy study of the catalytic mechanism of Trypanosoma cruzi trans-sialidase. From the Michaelis complex to the covalent intermediate. Biochemistry. 50: 10150-8. PMID 22007596 DOI: 10.1021/Bi2009618 |
0.328 |
|
| 2011 |
Rodriguez Limardo RG, Ferreiro DN, Roitberg AE, Marti MA, Turjanski AG. p38γ activation triggers dynamical changes in allosteric docking sites. Biochemistry. 50: 1384-95. PMID 21235211 DOI: 10.1021/Bi1007518 |
0.313 |
|
| 2011 |
Nelson T, Fernandez-Alberti S, Chernyak V, Roitberg AE, Tretiak S. Nonadiabatic excited-state molecular dynamics modeling of photoinduced dynamics in conjugated molecules. The Journal of Physical Chemistry. B. 115: 5402-14. PMID 21218841 DOI: 10.1021/Jp109522G |
0.385 |
|
| 2011 |
Pierdominici-Sottile G, Roitberg AE. Proton transfer facilitated by ligand binding. An energetic analysis of the catalytic mechanism of Trypanosoma cruzi trans-sialidase. Biochemistry. 50: 836-42. PMID 21162542 DOI: 10.1021/Bi101648Z |
0.333 |
|
| 2010 |
Sindhikara DJ, Emerson DJ, Roitberg AE. Exchange Often and Properly in Replica Exchange Molecular Dynamics. Journal of Chemical Theory and Computation. 6: 2804-8. PMID 26616081 DOI: 10.1021/Ct100281C |
0.751 |
|
| 2010 |
Capece L, Arrar M, Roitberg AE, Yeh SR, Marti MA, Estrin DA. Substrate stereo-specificity in tryptophan dioxygenase and indoleamine 2,3-dioxygenase. Proteins. 78: 2961-72. PMID 20715188 DOI: 10.1002/Prot.22819 |
0.328 |
|
| 2010 |
Lawrenz M, Wereszczynski J, Amaro R, Walker R, Roitberg A, McCammon JA. Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy Proteins: Structure, Function and Bioinformatics. 78: 2523-2532. PMID 20602360 DOI: 10.1002/Prot.22761 |
0.542 |
|
| 2010 |
Meng Y, Roitberg AE. Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model. Journal of Chemical Theory and Computation. 6: 1401-1412. PMID 20514364 DOI: 10.1021/Ct900676B |
0.72 |
|
| 2010 |
Fernandez-Alberti S, Kleiman VD, Tretiak S, Roitberg AE. Unidirectional energy transfer in conjugated molecules: The crucial role of high-frequency C ≡ C bonds Journal of Physical Chemistry Letters. 1: 2699-2704. DOI: 10.1021/Jz100794Z |
0.34 |
|
| 2010 |
Palma JL, Atas E, Hardison L, Marder TB, Collings JC, Beeby A, Melinger JS, Krause JL, Kleiman VD, Roitberg AE. Electronic spectra of the nanostar dendrimer: Theory and experiment Journal of Physical Chemistry C. 114: 20702-20712. DOI: 10.1021/Jp1062918 |
0.374 |
|
| 2010 |
Sindhikara DJ, Emerson DJ, Roitberg AE. Exchange often and properly in replica exchange molecular dynamics Journal of Chemical Theory and Computation. 6: 2804-2808. DOI: 10.1021/ct100281c |
0.735 |
|
| 2009 |
Sindhikara DJ, Kim S, Voter AF, Roitberg AE. Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules. Journal of Chemical Theory and Computation. 5: 1624-31. PMID 26609854 DOI: 10.1021/Ct800573M |
0.775 |
|
| 2009 |
Torras J, Seabra Gde M, Roitberg AE. A Multiscale Treatment of Angeli's Salt Decomposition. Journal of Chemical Theory and Computation. 5: 37-46. PMID 26609819 DOI: 10.1021/Ct800236D |
0.323 |
|
| 2009 |
Wang XS, Roitberg AE, Richards NG. Computational studies of ammonia channel function in glutamine 5'-phosphoribosylpyrophosphate amidotransferase. Biochemistry. 48: 12272-82. PMID 19921932 DOI: 10.1021/Bi901521D |
0.331 |
|
| 2009 |
Sindhikara DJ, Roitberg AE, Merz KM. Apo and nickel-bound forms of the Pyrococcus horikoshii species of the metalloregulatory protein: NikR characterized by molecular dynamics simulations. Biochemistry. 48: 12024-33. PMID 19891498 DOI: 10.1021/Bi9013352 |
0.747 |
|
| 2009 |
Seabra Gde M, Walker RC, Roitberg AE. Are current semiempirical methods better than force fields? A study from the thermodynamics perspective. The Journal of Physical Chemistry. A. 113: 11938-48. PMID 19848431 DOI: 10.1021/Jp903474V |
0.356 |
|
| 2009 |
Williams DE, Peters MB, Wang B, Roitberg AE, Merz KM. AM1 parameters for the prediction of 1H and 13C NMR chemical shifts in proteins. The Journal of Physical Chemistry. A. 113: 11550-9. PMID 19799435 DOI: 10.1021/Jp9028722 |
0.308 |
|
| 2009 |
Fernandez-Alberti S, Kleiman VD, Tretiak S, Roitberg AE. Nonadiabatic molecular dynamics simulations of the energy transfer between building blocks in a phenylene ethynylene dendrimer. The Journal of Physical Chemistry. A. 113: 7535-42. PMID 19378966 DOI: 10.1021/Jp900904Q |
0.407 |
|
| 2009 |
Dolghih E, Ortiz W, Kim S, Krueger BP, Krause JL, Roitberg AE. Theoretical studies of short polyproline systems: recalibration of a molecular ruler. The Journal of Physical Chemistry. A. 113: 4639-46. PMID 19265388 DOI: 10.1021/Jp811395R |
0.64 |
|
| 2009 |
Demir O, Roitberg AE. Modulation of catalytic function by differential plasticity of the active site: case study of Trypanosoma cruzi trans-sialidase and Trypanosoma rangeli sialidase. Biochemistry. 48: 3398-406. PMID 19216574 DOI: 10.1021/Bi802230Y |
0.637 |
|
| 2009 |
Martí MA, Estrin DA, Roitberg AE. Molecular basis for the pH dependent structural transition of Nitrophorin 4. The Journal of Physical Chemistry. B. 113: 2135-42. PMID 19170552 DOI: 10.1021/Jp808055E |
0.405 |
|
| 2009 |
Swails JM, Meng Y, Walker FA, Marti MA, Estrin DA, Roitberg AE. pH-dependent mechanism of nitric oxide release in nitrophorins 2 and 4. The Journal of Physical Chemistry. B. 113: 1192-201. PMID 19159340 DOI: 10.1021/Jp806906X |
0.763 |
|
| 2009 |
Sindhikara DJ, Kim S, Voter AF, Roitberg AE. Bad seeds sprout perilous dynamics: Stochastic thermostat induced trajectory synchronization in biomolecules Journal of Chemical Theory and Computation. 5: 1624-1631. DOI: 10.1021/ct800573m |
0.76 |
|
| 2009 |
Long JR, Mehta AK, Meng Y, Roitberg A, Antharam V, Ganesh O, Farver S. The Structural Plasticity Of Lung Surfactant Peptide KL4 In Lipid Membranes Biophysical Journal. 96: 159a. DOI: 10.1016/J.Bpj.2008.12.725 |
0.673 |
|
| 2008 |
Castro MA, Roitberg AE, Cukiernik FD. Theoretical and experimental studies of diruthenium tetracarboxylates structure, spectroscopy, and electrochemistry. Inorganic Chemistry. 47: 4682-90. PMID 18459726 DOI: 10.1021/Ic702505Z |
0.33 |
|
| 2008 |
Torras J, Seabra Gde M, Deumens E, Trickey SB, Roitberg AE. A versatile AMBER-Gaussian QM/MM interface through PUPIL. Journal of Computational Chemistry. 29: 1564-73. PMID 18270957 DOI: 10.1002/Jcc.20915 |
0.317 |
|
| 2008 |
Sindhikara D, Meng Y, Roitberg AE. Exchange frequency in replica exchange molecular dynamics. The Journal of Chemical Physics. 128: 024103. PMID 18205439 DOI: 10.1063/1.2816560 |
0.773 |
|
| 2008 |
Kim S, Roitberg AE. Simulating temperature jumps for protein folding. The Journal of Physical Chemistry. B. 112: 1525-32. PMID 18193855 DOI: 10.1021/Jp0727392 |
0.682 |
|
| 2008 |
Crecca CR, Roitberg AE. Using distances between α-carbons to predict protein structure International Journal of Quantum Chemistry. 108: 2782-2792. DOI: 10.1002/Qua.21769 |
0.755 |
|
| 2008 |
Crecca C, Roitberg AE. Using the Rosetta algorithm and selected inter-residue distances to predict protein structure International Journal of Quantum Chemistry. 108: 2793-2802. DOI: 10.1002/Qua.21768 |
0.755 |
|
| 2007 |
de M Seabra G, Walker RC, Elstner M, Case DA, Roitberg AE. Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. The Journal of Physical Chemistry. A. 111: 5655-64. PMID 17521173 DOI: 10.1021/Jp070071L |
0.371 |
|
| 2007 |
Roitberg AE, Okur A, Simmerling C. Coupling of replica exchange simulations to a non-Boltzmann structure reservoir. The Journal of Physical Chemistry. B. 111: 2415-8. PMID 17300191 DOI: 10.1021/Jp068335B |
0.357 |
|
| 2007 |
Alkis S, Jiang P, Wang LL, Roitberg AE, Cheng HP, Krause JL. Molecular dynamics simulations of alkanethiol monolayers with azobenzene molecules on the Au(111) surface Journal of Physical Chemistry C. 111: 14743-14752. DOI: 10.1021/Jp068471G |
0.352 |
|
| 2007 |
Dolghih E, Roitberg AE, Krause JL. Fluorescence resonance energy transfer in dye-labeled DNA Journal of Photochemistry and Photobiology a: Chemistry. 190: 321-327. DOI: 10.1016/J.Jphotochem.2006.11.009 |
0.309 |
|
| 2007 |
Mujica V, Nitzan A, Mao Y, Davis W, Kemp M, Roitberg A, Ratner MA. Electron Transfer in Molecules and Molecular Wires: Geometry Dependence, Coherent Transfer, and Control Advances in Chemical Physics. 107: 403-429. DOI: 10.1002/9780470141663.Ch7 |
0.422 |
|
| 2006 |
Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 65: 712-25. PMID 16981200 DOI: 10.1002/Prot.21123 |
0.339 |
|
| 2006 |
Crecca CR, Roitberg AE. Theoretical study of the isomerization mechanism of azobenzene and disubstituted azobenzene derivatives. The Journal of Physical Chemistry. A. 110: 8188-203. PMID 16805507 DOI: 10.1021/Jp057413C |
0.747 |
|
| 2006 |
Xiong H, Crespo A, Marti M, Estrin D, Roitberg AE. Free energy calculations with non-equilibrium methods: Applications of the Jarzynski relationship Theoretical Chemistry Accounts. 116: 338-346. DOI: 10.1007/S00214-005-0072-2 |
0.341 |
|
| 2005 |
Ortiz W, Krueger BP, Kleiman VD, Krause JL, Roitberg AE. Energy transfer in the nanostar: the role of coulombic coupling and dynamics. The Journal of Physical Chemistry. B. 109: 11512-9. PMID 16852410 DOI: 10.1021/Jp050611J |
0.379 |
|
| 2005 |
Crespo A, Martí MA, Estrin DA, Roitberg AE. Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase. Journal of the American Chemical Society. 127: 6940-1. PMID 15884923 DOI: 10.1021/Ja0452830 |
0.328 |
|
| 2005 |
Roitberg AE. Chapter 8 Nonequilibrium Approaches to Free Energy Calculations Annual Reports in Computational Chemistry. 1: 103-111. DOI: 10.1016/S1574-1400(05)01008-X |
0.328 |
|
| 2003 |
Crespo A, Scherlis DA, Martí MA, Ordejón P, Roitberg AE, Estrin DA. A DFT-based QM-MM approach designed for the treatment of large molecular systems: Application to chorismate mutase Journal of Physical Chemistry B. 107: 13728-13736. DOI: 10.1021/Jp036236H |
0.341 |
|
| 2003 |
Worthington SE, Roitberg AE, Krauss M. Kinetic isotope effects in the active site of B. subtilis chorismate mutase International Journal of Quantum Chemistry. 94: 287-292. DOI: 10.1002/Qua.10641 |
0.322 |
|
| 2002 |
Simmerling C, Strockbine B, Roitberg AE. All-atom structure prediction and folding simulations of a stable protein. Journal of the American Chemical Society. 124: 11258-9. PMID 12236726 DOI: 10.1021/Ja0273851 |
0.364 |
|
| 2002 |
González Lebrero MC, Bikiel DE, Dolores Elola M, Estrin DA, Roitberg AE. Solvent-induced symmetry breaking of nitrate ion in aqueous clusters: A quantum-classical simulation study Journal of Chemical Physics. 117: 2718. DOI: 10.1063/1.1490578 |
0.337 |
|
| 2002 |
Mayhew MP, Roitberg AE, Tewari Y, Holden MJ, Vanderah DJ, Vilker VL. Benzocycloarene hydroxylation by P450 biocatalysis New Journal of Chemistry. 26: 35-42. DOI: 10.1039/B107584P |
0.302 |
|
| 2001 |
Wang L, Roitberg AE, Meuse CW, Gaigalas AK. Raman and FTIR spectroscopies of fluorescein in solutions. Spectrochimica Acta Part a: Molecular and Biomolecular Spectroscopy. 57: 1781-1791. PMID 11506029 DOI: 10.1016/S1386-1425(01)00408-5 |
0.302 |
|
| 2000 |
Mujica V, Roitberg AE, Ratner M. Molecular wire conductance: Electrostatic potential spatial profile Journal of Chemical Physics. 112: 6834-6839. DOI: 10.1063/1.481258 |
0.414 |
|
| 1999 |
Yaliraki SN, Roitberg AE, Gonzalez C, Mujica V, Ratner MA. The injecting energy at molecule/metal interfaces: Implications for conductance of molecular junctions from an ab initio molecular description The Journal of Chemical Physics. 111: 6997-7002. DOI: 10.1063/1.480096 |
0.473 |
|
| 1998 |
Kemp M, Mujica V, Roitberg A, Ratner MA. Molecular Wire Interconnects: Chemical Structural Control, Resonant Tunneling and
Length Dependence Vlsi Design. 8: 65-74. DOI: 10.1155/1998/73516 |
0.462 |
|
| 1998 |
Ratner MA, Davis B, Kemp M, Mujica V, Roitberg A, Yaliraki S. Molecular wires: Charge transport, mechanisms, and control Annals of the New York Academy of Sciences. 852: 22-37. DOI: 10.1111/J.1749-6632.1998.Tb09862.X |
0.446 |
|
| 1998 |
Roitberg AE. Binding and electron transfer between putidaredoxin and cytochrome P450cam. Theory and experiments Journal of the American Chemical Society. 120: 8927-8932. DOI: 10.1021/Ja9739906 |
0.304 |
|
| 1997 |
Roitberg AE. A molecular dynamics study of Fe2S2 putidaredoxin: multiple conformations of the C-terminal region. Biophysical Journal. 73: 2138-48. PMID 9336209 DOI: 10.1016/S0006-3495(97)78244-4 |
0.412 |
|
| 1997 |
Roitberg AE, Gerber RB, Ratner MA. A Vibrational Eigenfunction of a Protein: Anharmonic Coupled-Mode Ground and Fundamental Excited States of BPTI The Journal of Physical Chemistry B. 101: 1700-1706. DOI: 10.1021/Jp9629194 |
0.574 |
|
| 1996 |
Norris LS, Ratner MA, Roitberg AE, Gerber RB. Mo/ller–Plesset perturbation theory applied to vibrational problems The Journal of Chemical Physics. 105: 11261-11267. DOI: 10.1063/1.472922 |
0.591 |
|
| 1996 |
Mujica V, Kemp M, Roitberg A, Ratner M. Current‐voltage characteristics of molecular wires: Eigenvalue staircase, Coulomb blockade, and rectification The Journal of Chemical Physics. 104: 7296-7305. DOI: 10.1063/1.471396 |
0.43 |
|
| 1996 |
Kemp M, Roitberg A, Mujica V, Wanta T, Ratner MA. Molecular Wires: Extended Coupling and Disorder Effects The Journal of Physical Chemistry. 100: 8349-8355. DOI: 10.1021/Jp952431N |
0.416 |
|
| 1995 |
Roitberg A, Gerber RB, Elber R, Ratner MA. Anharmonic wave functions of proteins: quantum self-consistent field calculations of BPTI. Science (New York, N.Y.). 268: 1319-22. PMID 7539156 DOI: 10.1126/Science.7539156 |
0.683 |
|
| 1995 |
Elber R, Roitberg A, Simmerling C, Goldstein R, Li H, Verkhivker G, Keasar C, Zhang J, Ulitsky A. MOIL: A program for simulations of macromolecules Computer Physics Communications. 91: 159-189. DOI: 10.1016/0010-4655(95)00047-J |
0.599 |
|
| 1994 |
Roitberg AE, Gerber RB, Ratner MA. A perturbed‐mean‐field approach to the decay rates of excited vibrational states in extended systems: An application toI2(Ne)n The Journal of Chemical Physics. 100: 4355-4366. DOI: 10.1063/1.466318 |
0.575 |
|
| 1994 |
Cheong A, Roitberg AE, Mujica V, Ratner MA. Resonances and interference effects on the effective electronic coupling in electron transfer Journal of Photochemistry and Photobiology, a: Chemistry. 82: 81-86. DOI: 10.1016/1010-6030(94)02020-5 |
0.448 |
|
| 1991 |
Roitberg A, Elber R. Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations Journal of Chemical Physics. 95: 9277-9287. DOI: 10.1063/1.461157 |
0.565 |
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