Adrian Enrique Roitberg - Publications

Affiliations: 
University of Florida, Gainesville, Gainesville, FL, United States 
Area:
Computational Chemistry

125 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
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  0.32
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  0.36
2016 Blanco Capurro JI, Hopkins CW, Pierdominici-Sottile G, Gonzalez Lebrero MC, Roitberg AE, Marti MA. Theoretical Insights into the Reaction and Inhibition Mechanism of Metal-Independent Retaining Glycosyltransferase Responsible for Mycothiol Biosynthesis. The Journal of Physical Chemistry. B. PMID 27935720 DOI: 10.1021/acs.jpcb.6b10130  0.44
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  0.44
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  0.44
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  0.36
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  1
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  1
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  1
2015 Di Russo NV, Bruner SD, Roitberg AE. Applicability of fluorescence-based sensors to the determination of kinetic parameters for O₂ in oxygenases. Analytical Biochemistry. 475: 53-5. PMID 25637681 DOI: 10.1016/j.ab.2015.01.009  1
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  1
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  1
2015 Goldfarb NE, Ohanessian M, Biswas S, McGee TD, Mahon BP, Ostrov DA, Garcia J, Tang Y, McKenna R, Roitberg A, Dunn BM. Defective hydrophobic sliding mechanism and active site expansion in HIV-1 protease drug resistant variant Gly48Thr/Leu89Met: mechanisms for the loss of saquinavir binding potency. Biochemistry. 54: 422-33. PMID 25513833 DOI: 10.1021/bi501088e  1
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 Journal of Chemical Physics. 142. DOI: 10.1063/1.4922925  1
2015 Silva JRA, Govender T, Maguire GEM, Kruger HG, Lameira J, Roitberg AE, Alves CN. Simulating the inhibition reaction of Mycobacterium tuberculosis L,D-transpeptidase 2 by carbapenems Chemical Communications. 51: 12560-12562. DOI: 10.1039/c5cc03202d  1
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: 1864-1874. DOI: 10.1021/ct5010406  1
2015 Zhao X, Watkins DL, Galindo JF, Shewmon NT, Roitberg AE, Xue J, Castellano RK, Perry SS. Hydrogen bond directed assembly of oligothiophene/fullerene superstructures on Au(1 1 1) Organic Electronics: Physics, Materials, Applications. 19: 61-69. DOI: 10.1016/j.orgel.2015.01.022  1
2015 Shewmon NT, Watkins DL, Galindo JF, Zerdan RB, Chen J, Keum J, Roitberg AE, Xue J, Castellano RK. Enhancement in Organic Photovoltaic Efficiency through the Synergistic Interplay of Molecular Donor Hydrogen Bonding and π-Stacking Advanced Functional Materials. DOI: 10.1002/adfm.201501815  1
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  1
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  1
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  1
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  1
2014 Soler MA, Nelson T, Roitberg AE, Tretiak S, Fernandez-Alberti S. Signature of nonadiabatic coupling in excited-state vibrational modes. The Journal of Physical Chemistry. A. 118: 10372-9. PMID 24844735 DOI: 10.1021/jp503350k  1
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  1
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  1
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  1
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  1
2014 Pierdominici-Sottile G, Palma J, Roitberg AE. Free-energy computations identify the mutations required to confer trans-sialidase activity into Trypanosoma rangeli sialidase. Proteins. 82: 424-35. PMID 23999862 DOI: 10.1002/prot.24408  1
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: 4609-4617. DOI: 10.1021/ct500672d  1
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  0.68
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  1
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  1
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  1
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  1
2013 Oliveira A, Allegri A, Bidon-Chanal A, Knipp M, Roitberg AE, Abbruzzetti S, Viappiani C, Luque FJ. Kinetics and computational studies of ligand migration in nitrophorin 7 and its Δ1-3 mutant. Biochimica Et Biophysica Acta. 1834: 1711-21. PMID 23624263 DOI: 10.1016/j.bbapap.2013.04.009  1
2013 Stedwell CN, Galindo JF, Roitberg AE, Polfer NC. Structures of biomolecular ions in the gas phase probed by infrared light sources. Annual Review of Analytical Chemistry (Palo Alto, Calif.). 6: 267-85. PMID 23560933 DOI: 10.1146/annurev-anchem-062012-092700  1
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  1
2013 Boechi L, Arrar M, Martí 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  1
2013 Stedwell CN, Galindo JF, Gulyuz K, Roitberg AE, Polfer NC. Crown complexation of protonated amino acids: influence on IRMPD spectra. The Journal of Physical Chemistry. A. 117: 1181-8. PMID 22891977 DOI: 10.1021/jp305263b  1
2013 Zhu X, Nepomnyashchii AB, Roitberg AE, Parkinson BA, Schanze KS. Photosensitization of single-crystal ZnO by a conjugated polyelectrolyte designed to avoid aggregation Journal of Physical Chemistry Letters. 4: 3216-3220. DOI: 10.1021/jz401636s  1
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  1
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: 4470-4480. DOI: 10.1021/ct400471m  1
2013 Sabri Dashti D, Roitberg AE. Optimization of umbrella sampling replica exchange molecular dynamics by replica positioning Journal of Chemical Theory and Computation. 9: 4692-4699. DOI: 10.1021/ct400366h  1
2013 Castro MA, Roitberg AE, Cukiernik FD. Electronic delocalization in coordination polymers based on bimetallic carboxylates Journal of Chemical Theory and Computation. 9: 2609-2616. DOI: 10.1021/ct400179t  1
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  1
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  0.88
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  0.8
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  1
2012 Di Russo NV, Estrin DA, Martí 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  1
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  1
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  1
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  1
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  1
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  1
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  1
2012 Feng F, Lee SH, Cho SW, Kömürlü S, McCarley TD, Roitberg A, Kleiman VD, Schanze KS. Conjugated polyelectrolyte dendrimers: Aggregation, photophysics, and amplified quenching Langmuir. 28: 16679-16691. DOI: 10.1021/la303641m  1
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  1
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  1
2012 Mulholland AJ, Roitberg AE, Tuñón I. Enzyme dynamics and catalysis in the mechanism of DNA polymerase Theoretical Chemistry Accounts. 131: 1-4. DOI: 10.1007/s00214-012-1286-8  1
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  1
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  1
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  1
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  1
2011 Defelipe LA, Dolghih E, Roitberg AE, Nouzova M, Mayoral JG, Noriega FG, Turjanski AG. Juvenile hormone synthesis: "esterify then epoxidize" or "epoxidize then esterify"? Insights from the structural characterization of juvenile hormone acid methyltransferase. Insect Biochemistry and Molecular Biology. 41: 228-35. PMID 21195763 DOI: 10.1016/j.ibmb.2010.12.008  1
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  1
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  0.76
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2009 Mayoral JG, Nouzova M, Yoshiyama M, Shinoda T, Hernandez-Martinez S, Dolghih E, Turjanski AG, Roitberg AE, Priestap H, Perez M, Mackenzie L, Li Y, Noriega FG. Molecular and functional characterization of a juvenile hormone acid methyltransferase expressed in the corpora allata of mosquitoes. Insect Biochemistry and Molecular Biology. 39: 31-7. PMID 18984053 DOI: 10.1016/j.ibmb.2008.09.010  1
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  1
2009 Torras J, De Seabra GM, Roitberg AE. A multiscale treatment of Angeli's salt decomposition Journal of Chemical Theory and Computation. 5: 37-46. DOI: 10.1021/ct800236d  1
2008 McGee TD, Edwards J, Roitberg AE. Preliminary molecular dynamic simulations of the estrogen receptor alpha ligand binding domain from antagonist to apo. International Journal of Environmental Research and Public Health. 5: 111-4. PMID 18678925 DOI: 10.3390/ijerph2008050014  1
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  1
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  1
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  1
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  1
2008 Martí MA, González Lebrero MC, Roitberg AE, Estrin DA. Bond or cage effect: how nitrophorins transport and release nitric oxide. Journal of the American Chemical Society. 130: 1611-8. PMID 18189390 DOI: 10.1021/ja075565a  1
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  1
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  1
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  1
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  1
2007 Doucet D, Roitberg A, Hagen SJ. Kinetics of internal-loop formation in polypeptide chains: A simulation study Biophysical Journal. 92: 2281-2289. PMID 17208979 DOI: 10.1529/biophysj.106.092379  1
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  1
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  1
2006 Crespo A, Martí MA, Roitberg AE, Amzel LM, Estrin DA. The catalytic mechanism of peptidylglycine alpha-hydroxylating monooxygenase investigated by computer simulation. Journal of the American Chemical Society. 128: 12817-28. PMID 17002377 DOI: 10.1021/ja062876x  1
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  1
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  1
2006 Smith N, Roitberg AE, Rivera E, Howard A, Holden MJ, Mayhew M, Kaistha S, Gallagher DT. Structural analysis of ligand binding and catalysis in chorismate lyase. Archives of Biochemistry and Biophysics. 445: 72-80. PMID 16343413 DOI: 10.1016/j.abb.2005.10.026  1
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  1
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  1
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  1
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  1
2004 Zhang C, Du MH, Cheng HP, Zhang XG, Roitberg AE, Krause JL. Coherent electron transport through an azobenzene molecule: a light-driven molecular switch. Physical Review Letters. 92: 158301. PMID 15169322 DOI: 10.1103/PhysRevLett.92.158301  1
2004 Ortiz W, Roitberg AE, Krause JL. Molecular dynamics of poly(benzylphenyl ether) dendrimers: Effects of backfolding on förster energy-transfer rates Journal of Physical Chemistry B. 108: 8218-8225. DOI: 10.1021/jp0379998  1
2004 Roitberg A, Simmerling C. Journal of Molecular Graphics and Modelling: Foreword Journal of Molecular Graphics and Modelling. 22: 317. DOI: 10.1016/j.jmgm.2004.03.015  1
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  1
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.  1
2002 Qiu L, Pabit SA, Roitberg AE, Hagen SJ. Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros. Journal of the American Chemical Society. 124: 12952-3. PMID 12405814 DOI: 10.1021/ja0279141  1
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  1
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  1
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  1
2001 Wang GM, Blaisten-Barojas E, Roitberg AE, Martin TP. Strontium clusters: Many-body potential, energetics, and structural transitions Journal of Chemical Physics. 115: 3640-3646. DOI: 10.1063/1.1384454  1
2001 Worthington SE, Roitberg AE, Krauss M. An MD/QM study of the chorismate mutase-catalyzed Claisen rearrangement reaction Journal of Physical Chemistry B. 105: 7087-7095. DOI: 10.1021/jp010227w  1
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  1
2000 Roitberg AE, Worthington SE, Holden MJ, Mayhew MP, Krauss M. The electronic spectrum of the prephenate dianion. An experimental and theoretical (MD/QM) comparison Journal of the American Chemical Society. 122: 7312-7316. DOI: 10.1021/ja9945358  1
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 Journal of Chemical Physics. 111: 6997-7002.  1
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  1
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  1
1997 Roitberg AE, Benny Gerber R, Ratner MA. A vibrational eigenfunction of a protein: Anharmonic coupled-mode ground and fundamental excited states of BPTI Journal of Physical Chemistry B. 101: 1700-1706.  1
1996 Norris LS, Ratner MA, Roitberg AE, Gerber RB. Møller-Plesset perturbation theory applied to vibrational problems Journal of Chemical Physics. 105: 11261-11267.  1
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  1
1994 Roitberg AE, Benny Gerber R, Ratner MA. A perturbed-mean-field approach to the decay rates of excited vibrational states in extended systems: An application to I2(Ne)n The Journal of Chemical Physics. 100: 4355-4366.  1
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