☰

Ron Elber, PhD - Publications

Affiliations: 
Chemistry University of Texas at Austin, Austin, Texas, U.S.A. 
Area:
Computational Chemistry
Website:
http://clsb.ices.utexas.edu/web/index.html
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156 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 Kirmizialtin S, Pitici F, Cardenas AE, Elber R, Thirumalai D. Dramatic Shape Changes Occur as Cytochrome Folds. The Journal of Physical Chemistry. B. PMID 32840372 DOI: 10.1021/Acs.Jpcb.0C05802  0.395
2020 Wang H, Elber R. Milestoning with wind: Exploring the impact of a biasing potential in exact calculation of kinetics. The Journal of Chemical Physics. 152: 224105. PMID 32534551 DOI: 10.1063/5.0011050  0.315
2020 Fathizadeh A, Valentine M, Baiz CR, Elber R. Phase Transition in a Heterogeneous Membrane: Atomically Detailed Picture. The Journal of Physical Chemistry Letters. 5263-5267. PMID 32525318 DOI: 10.1021/Acs.Jpclett.0C01255  0.345
2020 Templeton C, Elber R. A Simple and Analytical Model of RNA Collapse. The Journal of Physical Chemistry. B. PMID 32459501 DOI: 10.1021/Acs.Jpcb.0C03584  0.323
2020 Elber R. Milestoning: An Efficient Approach for Atomically Detailed Simulations of Kinetics in Biophysics. Annual Review of Biophysics. 49: 69-85. PMID 32375019 DOI: 10.1146/Annurev-Biophys-121219-081528  0.392
2020 Wang H, Huang N, Dangerfield T, Johnson KA, Gao J, Elber R. Exploring the Reaction Mechanism of HIV RT with a Nucleotide Substrate. The Journal of Physical Chemistry. B. PMID 32364738 DOI: 10.1021/Acs.Jpcb.0C02632  0.539
2020 Narayan B, Yuan Y, Fathizadeh A, Elber R, Buchete NV. Long-time methods for molecular dynamics simulations: Markov State Models and Milestoning. Progress in Molecular Biology and Translational Science. 170: 215-237. PMID 32145946 DOI: 10.1016/Bs.Pmbts.2020.01.002  0.414
2020 Wei W, Elber R. ScMile: A Script to Investigate Kinetics with Short Time Molecular Dynamics Trajectories and the Milestoning Theory. Journal of Chemical Theory and Computation. PMID 31922745 DOI: 10.1021/Acs.Jctc.9B01030  0.357
2020 Ma P, Cardenas AE, Chaudhari M, Elber R, Rempe SL. Translocation of Anthrax Lethal Factor: Perspectives from Atomic Molecular Dynamics Simulations Biophysical Journal. 118: 299a. DOI: 10.1016/J.Bpj.2019.11.1693  0.326
2019 Narayan B, Fathizadeh A, Templeton C, He P, Arasteh S, Elber R, Buchete NV, Levy RM. The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning. Biochimica Et Biophysica Acta. General Subjects. 129508. PMID 31884066 DOI: 10.1016/J.Bbagen.2019.129508  0.452
2019 Fathizadeh A, Kogan M, Anderson CM, Webb LJ, Elber R. Defect Assisted Permeation Through a Phospholipid Membrane: Experimental and Computational Study of the Peptide WKW. The Journal of Physical Chemistry. B. PMID 31304755 DOI: 10.1021/Acs.Jpcb.9B05414  0.302
2019 Ma P, Cardenas AE, Chaudhari M, Elber R, Rempe SL. Early Translocation of Anthrax Lethal Factor: Kinetics from Molecular Dynamics Simulations and Milestoning Theory Biophysical Journal. 116: 436a. DOI: 10.1016/J.Bpj.2018.11.2346  0.309
2018 Chen YL, Lee T, Elber R, Pollack L. Conformations of an RNA Helix-Junction-Helix Construct Revealed by SAXS Refinement of MD Simulations. Biophysical Journal. PMID 30558889 DOI: 10.1016/J.Bpj.2018.11.020  0.367
2018 Templeton C, Elber R. Why does RNA collapse? The importance of water in a simulation study of helix-junction-helix systems. Journal of the American Chemical Society. PMID 30465606 DOI: 10.1021/Jacs.8B11111  0.336
2018 Ma P, Cardenas AE, Chaudhari MI, Elber R, Rempe SB. Probing Translocation in Mutants of the Anthrax Channel: Atomically Detailed Simulations with Milestoning. The Journal of Physical Chemistry. B. PMID 30338689 DOI: 10.1021/Acs.Jpcb.8B08304  0.311
2018 Fathizadeh A, Elber R. A mixed alchemical and equilibrium dynamics to simulate heterogeneous dense fluids: Illustrations for Lennard-Jones mixtures and phospholipid membranes. The Journal of Chemical Physics. 149: 072325. PMID 30134684 DOI: 10.1063/1.5027078  0.332
2018 Plumridge A, Katz AM, Calvey GD, Elber R, Kirmizialtin S, Pollack L. Revealing the distinct folding phases of an RNA three-helix junction. Nucleic Acids Research. PMID 29762712 DOI: 10.1093/Nar/Gky363  0.311
2017 Elber R. A new paradigm for atomically detailed simulations of kinetics in biophysical systems. Quarterly Reviews of Biophysics. 50: e8. PMID 29233220 DOI: 10.1017/S0033583517000063  0.381
2017 Templeton C, Chen SH, Fathizadeh A, Elber R. Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways. The Journal of Chemical Physics. 147: 152718. PMID 29055297 DOI: 10.1063/1.4986298  0.371
2017 Ma P, Cardenas AE, Chaudhari MI, Elber R, Rempe SB. The Impact of Protonation on Early Translocation of Anthrax Lethal Factor: Kinetics From Molecular Dynamics Simulations and Milestoning Theory. Journal of the American Chemical Society. PMID 29019235 DOI: 10.1021/Jacs.7B07419  0.331
2017 Atiş M, Johnson KA, Elber R. Pyrophosphate Release in the Protein HIV Reverse Transcriptase. The Journal of Physical Chemistry. B. PMID 28926712 DOI: 10.1021/Acs.Jpcb.7B08320  0.391
2017 Elber R, Bello-Rivas JM, Ma P, Cardenas AE, Fathizadeh A. Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning. Entropy (Basel, Switzerland). 19. PMID 28757794 DOI: 10.3390/E19050219  0.361
2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  0.514
2016 Cardenas AE, Elber R. Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning. The Journal of Physical Chemistry. B. PMID 27016332 DOI: 10.1021/Acs.Jpcb.6B01890  0.329
2016 Elber R. Perspective: Computer simulations of long time dynamics. The Journal of Chemical Physics. 144: 060901. PMID 26874473 DOI: 10.1063/1.4940794  0.334
2015 Di Pierro M, Elber R, Leimkuhler B. A Stochastic Algorithm for the Isobaric-Isothermal Ensemble with Ewald Summations for All Long Range Forces. Journal of Chemical Theory and Computation. PMID 26616351 DOI: 10.1021/Acs.Jctc.5B00648  0.318
2015 Viswanath S, Dominguez L, Foster LS, Straub JE, Elber R. Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization. Proteins. PMID 26404856 DOI: 10.1002/Prot.24934  0.589
2015 Bello-Rivas JM, Elber R. Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning. Journal of Computational Chemistry. PMID 26265358 DOI: 10.1002/Jcc.24039  0.369
2015 Kirmizialtin S, Johnson KA, Elber R. Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition. The Journal of Physical Chemistry. B. PMID 26225641 DOI: 10.1016/J.Bpj.2015.11.410  0.351
2015 Elber R. From an SNP to a Disease: A Comprehensive Statistical Analysis. Structure (London, England : 1993). 23: 1155. PMID 26153880 DOI: 10.1016/J.Str.2015.06.005  0.326
2015 Chen SH, Meller J, Elber R. Comprehensive analysis of sequences of a protein switch. Protein Science : a Publication of the Protein Society. PMID 26073558 DOI: 10.1002/Pro.2723  0.349
2015 Cardenas AE, Shrestha R, Webb LJ, Elber R. Membrane Permeation of a Peptide: It Is Better to be Positive. The Journal of Physical Chemistry. B. 119: 6412-20. PMID 25941740 DOI: 10.1021/Acs.Jpcb.5B02122  0.34
2015 Mugnai ML, Shi Y, Keatinge-Clay AT, Elber R. Molecular dynamics studies of modular polyketide synthase ketoreductase stereospecificity. Biochemistry. 54: 2346-59. PMID 25835227 DOI: 10.1021/Bi501401G  0.318
2015 Shrestha R, Cardenas AE, Elber R, Webb LJ. Measurement of the membrane dipole electric field in DMPC vesicles using vibrational shifts of p-cyanophenylalanine and molecular dynamics simulations. The Journal of Physical Chemistry. B. 119: 2869-76. PMID 25602635 DOI: 10.1021/Jp511677J  0.308
2015 Mugnai ML, Elber R. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning. The Journal of Chemical Physics. 142: 014105. PMID 25573551 DOI: 10.1063/1.4904882  0.314
2015 Elber R. Two is a pair, three is a network. Biophysical Journal. 108: 22. PMID 25564848 DOI: 10.1016/J.Bpj.2014.11.1855  0.381
2015 Di Pierro M, Mugnai ML, Elber R. Optimizing potentials for a liquid mixture: a new force field for a tert-butanol and water solution. The Journal of Physical Chemistry. B. 119: 836-49. PMID 25066823 DOI: 10.1021/Jp505401M  0.304
2014 Viswanath S, Ravikant DV, Elber R. DOCK/PIERR: web server for structure prediction of protein-protein complexes. Methods in Molecular Biology (Clifton, N.J.). 1137: 199-207. PMID 24573483 DOI: 10.1007/978-1-4939-0366-5_14  0.359
2014 Chen SH, Elber R. The energy landscape of a protein switch. Physical Chemistry Chemical Physics : Pccp. 16: 6407-21. PMID 24473276 DOI: 10.1039/C3Cp55209H  0.419
2014 Elber R. Coil-Coil Under Load: Stability of Essential Machine Component Biophysical Journal. 106: 6. DOI: 10.1016/J.Bpj.2013.11.075  0.315
2014 Elber R, Cardenas AE. Molecular dynamics at extended timescales Israel Journal of Chemistry. DOI: 10.1002/Ijch.201400015  0.346
2013 Cardenas AE, Elber R. Computational study of peptide permeation through membrane: Searching for hidden slow variables. Molecular Physics. 111: 3565-3578. PMID 26203198 DOI: 10.1080/00268976.2013.842010  0.335
2013 Viswanath S, Kreuzer SM, Cardenas AE, Elber R. Analyzing milestoning networks for molecular kinetics: definitions, algorithms, and examples. The Journal of Chemical Physics. 139: 174105. PMID 24206285 DOI: 10.1063/1.4827495  0.32
2013 Kreuzer SM, Moon TJ, Elber R. Catch bond-like kinetics of helix cracking: network analysis by molecular dynamics and milestoning. The Journal of Chemical Physics. 139: 121902. PMID 24089714 DOI: 10.1063/1.4811366  0.308
2013 Kreuzer SM, Elber R. Coiled-coil response to mechanical force: global stability and local cracking. Biophysical Journal. 105: 951-61. PMID 23972847 DOI: 10.1016/J.Bpj.2013.05.064  0.331
2013 Meisburger SP, Sutton JL, Chen H, Pabit SA, Kirmizialtin S, Elber R, Pollack L. Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model. Biopolymers. 99: 1032-45. PMID 23606337 DOI: 10.1002/Bip.22265  0.314
2013 Viswanath S, Ravikant DV, Elber R. Improving ranking of models for protein complexes with side chain modeling and atomic potentials. Proteins. 81: 592-606. PMID 23180599 DOI: 10.1002/Prot.24214  0.352
2013 Di Pierro M, Elber R. Automated optimization of potential parameters Journal of Chemical Theory and Computation. 9: 3311-3320. DOI: 10.1016/J.Bpj.2013.11.2277  0.321
2012 Ruymgaart AP, Elber R. Revisiting Molecular Dynamics on a CPU/GPU system: Water Kernel and SHAKE Parallelization. Journal of Chemical Theory and Computation. 8: 4624-4636. PMID 23264758 DOI: 10.1021/Ct300324K  0.777
2012 Mugnai ML, Elber R. Thermodynamic Cycle Without Turning Off Self-Interactions: Formal Discussion and a Numerical Example. Journal of Chemical Theory and Computation. 8: 3022-3033. PMID 23028265 DOI: 10.1021/Ct3003817  0.307
2012 Kirmizialtin S, Nguyen V, Johnson KA, Elber R. How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations. Structure (London, England : 1993). 20: 618-27. PMID 22483109 DOI: 10.1016/J.Str.2012.02.018  0.351
2012 Kreuzer SM, Elber R, Moon TJ. Early events in helix unfolding under external forces: a milestoning analysis. The Journal of Physical Chemistry. B. 116: 8662-91. PMID 22471347 DOI: 10.1021/Jp300788E  0.354
2012 Cottone G, Lattanzi G, Ciccotti G, Elber R. Multiphoton absorption of myoglobin-nitric oxide complex: relaxation by D-NEMD of a stationary state. The Journal of Physical Chemistry. B. 116: 3397-410. PMID 22356468 DOI: 10.1021/Jp212148X  0.402
2012 Jas GS, Hegefeld WA, Májek P, Kuczera K, Elber R. Experiments and comprehensive simulations of the formation of a helical turn. The Journal of Physical Chemistry. B. 116: 6598-610. PMID 22335541 DOI: 10.1021/Jp211645S  0.73
2012 Cardenas AE, Jas GS, DeLeon KY, Hegefeld WA, Kuczera K, Elber R. Unassisted transport of N-acetyl-L-tryptophanamide through membrane: experiment and simulation of kinetics. The Journal of Physical Chemistry. B. 116: 2739-50. PMID 22313494 DOI: 10.1021/Jp2102447  0.301
2012 Burke S, Elber R. Super folds, networks, and barriers. Proteins. 80: 463-70. PMID 22095563 DOI: 10.1002/Prot.23212  0.35
2012 Mugnai ML, Elber R. Retaining the Self Interactions in Alchemical Free Energy Calculations Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.922  0.398
2012 Cardenas AE, DeLeon KY, Hegefeld WA, Kuczera K, Jas GS, Elber R. Unassisted Transport of Block Tryptophan through DOPC Membrane: Experiment and Simulation Biophysical Journal. 102: 713a-714a. DOI: 10.1016/J.Bpj.2011.11.3871  0.326
2012 Kirmizialtin S, Elber R, Johnson KA. Antlion Strategy for Enzyme Specificity Biophysical Journal. 102: 273a. DOI: 10.1016/J.Bpj.2011.11.1502  0.374
2011 Elber R, Ruymgaart AP, Hess B. SHAKE parallelization. The European Physical Journal. Special Topics. 200: 211-223. PMID 22368766 DOI: 10.1140/epjst/e2011-01525-9  0.783
2011 Ruymgaart AP, Cardenas AE, Elber R. MOIL-opt: Energy-Conserving Molecular Dynamics on a GPU/CPU system. Journal of Chemical Theory and Computation. 7: 3072-3082. PMID 22328867 DOI: 10.1021/Ct200360F  0.787
2011 Elber R. Progress at last. Structure (London, England : 1993). 19: 1725. PMID 22153491 DOI: 10.1016/J.Str.2011.11.005  0.309
2011 Ravikant DV, Elber R. Energy design for protein-protein interactions. The Journal of Chemical Physics. 135: 065102. PMID 21842951 DOI: 10.1063/1.3615722  0.38
2011 Kirmizialtin S, Elber R. Revisiting and computing reaction coordinates with Directional Milestoning. The Journal of Physical Chemistry. A. 115: 6137-48. PMID 21500798 DOI: 10.1021/Jp111093C  0.372
2011 Elber R. Simulations of allosteric transitions. Current Opinion in Structural Biology. 21: 167-72. PMID 21333527 DOI: 10.1016/J.Sbi.2011.01.012  0.351
2010 Májek P, Elber R. Milestoning without a Reaction Coordinate. Journal of Chemical Theory and Computation. 6: 1805-1817. PMID 20596240 DOI: 10.1021/Ct100114J  0.73
2010 Elber R, West A. Atomically detailed simulation of the recovery stroke in myosin by Milestoning. Proceedings of the National Academy of Sciences of the United States of America. 107: 5001-5. PMID 20194770 DOI: 10.1073/Pnas.0909636107  0.349
2010 Elber R. Ligand diffusion in globins: simulations versus experiment. Current Opinion in Structural Biology. 20: 162-7. PMID 20116995 DOI: 10.1016/J.Sbi.2010.01.002  0.383
2010 Cao B, Elber R. Computational exploration of the network of sequence flow between protein structures. Proteins. 78: 985-1003. PMID 19899165 DOI: 10.1002/Prot.22622  0.379
2010 Ravikant DV, Elber R. PIE-efficient filters and coarse grained potentials for unbound protein-protein docking. Proteins. 78: 400-19. PMID 19768784 DOI: 10.1002/Prot.22550  0.352
2009 Kuczera K, Jas GS, Elber R. Kinetics of helix unfolding: molecular dynamics simulations with milestoning. The Journal of Physical Chemistry. A. 113: 7461-73. PMID 19354256 DOI: 10.1021/Jp900407W  0.398
2009 Vallat BK, Pillardy J, Májek P, Meller J, Blom T, Cao B, Elber R. Building and assessing atomic models of proteins from structural templates: learning and benchmarks. Proteins. 76: 930-45. PMID 19326457 DOI: 10.1002/Prot.22401  0.741
2009 Májek P, Elber R. A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins. Proteins. 76: 822-36. PMID 19291741 DOI: 10.1002/Prot.22388  0.755
2009 Cao B, Elber R. Bistable Entropy Landscape of Sequences and Folds of Proteins Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.309  0.398
2008 Vanden-Eijnden E, Venturoli M, Ciccotti G, Elber R. On the assumptions underlying milestoning. The Journal of Chemical Physics. 129: 174102. PMID 19045328 DOI: 10.1063/1.2996509  0.331
2008 Steinberg MZ, Elber R, McLafferty FW, Gerber RB, Breuker K. Early structural evolution of native cytochrome c after solvent removal. Chembiochem : a European Journal of Chemical Biology. 9: 2417-23. PMID 18785672 DOI: 10.1002/Cbic.200800167  0.637
2008 Yu CN, Joachims T, Elber R, Pillardy J. Support vector training of protein alignment models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 867-80. PMID 18707536 DOI: 10.1089/Cmb.2007.0152  0.35
2008 Vallat BK, Pillardy J, Elber R. A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins. Proteins. 72: 910-28. PMID 18300226 DOI: 10.1002/Prot.21976  0.369
2008 Elber R, Gibson QH. Toward quantitative simulations of carbon monoxide escape pathways in myoglobin. The Journal of Physical Chemistry. B. 112: 6147-54. PMID 18205346 DOI: 10.1021/Jp0769779  0.332
2007 Steinberg MZ, Breuker K, Elber R, Gerber RB. The dynamics of water evaporation from partially solvated cytochrome c in the gas phase. Physical Chemistry Chemical Physics : Pccp. 9: 4690-7. PMID 17700870 DOI: 10.1039/B705905A  0.63
2007 Meyerguz L, Kleinberg J, Elber R. The network of sequence flow between protein structures. Proceedings of the National Academy of Sciences of the United States of America. 104: 11627-32. PMID 17596339 DOI: 10.1073/Pnas.0701393104  0.75
2007 West AM, Elber R, Shalloway D. Extending molecular dynamics time scales with milestoning: example of complex kinetics in a solvated peptide. The Journal of Chemical Physics. 126: 145104. PMID 17444753 DOI: 10.1063/1.2716389  0.412
2007 Elber R. A milestoning study of the kinetics of an allosteric transition: atomically detailed simulations of deoxy Scapharca hemoglobin. Biophysical Journal. 92: L85-7. PMID 17325010 DOI: 10.1529/Biophysj.106.101899  0.393
2006 Bai D, Elber R. Calculation of Point-to-Point Short-Time and Rare Trajectories with Boundary Value Formulation. Journal of Chemical Theory and Computation. 2: 484-94. PMID 26626659 DOI: 10.1021/Ct060028M  0.337
2006 Qiu J, Elber R. SSALN: an alignment algorithm using structure-dependent substitution matrices and gap penalties learned from structurally aligned protein pairs. Proteins. 62: 881-91. PMID 16385554 DOI: 10.1002/Prot.20854  0.563
2005 Qiu J, Elber R. Atomically detailed potentials to recognize native and approximate protein structures. Proteins. 61: 44-55. PMID 16080157 DOI: 10.1002/Prot.20585  0.578
2005 Elber R. Long-timescale simulation methods. Current Opinion in Structural Biology. 15: 151-6. PMID 15837172 DOI: 10.1016/J.Sbi.2005.02.004  0.345
2005 Weinbach Y, Elber R. Revisiting and parallelizing SHAKE Journal of Computational Physics. 209: 193-206. DOI: 10.1016/J.Jcp.2005.03.015  0.331
2005 Elber R. Computer simulations of protein folding: Classical trajectories by optimization of action Computer Physics Communications. 169: 277-283. DOI: 10.1016/J.Cpc.2005.03.063  0.438
2004 Faradjian AK, Elber R. Computing time scales from reaction coordinates by milestoning. The Journal of Chemical Physics. 120: 10880-9. PMID 15268118 DOI: 10.1063/1.1738640  0.353
2004 Meyerguz L, Grasso C, Kleinberg J, Elber R. Computational analysis of sequence selection mechanisms. Structure (London, England : 1993). 12: 547-57. PMID 15062078 DOI: 10.1016/J.Str.2004.02.018  0.75
2004 Teodorescu O, Galor T, Pillardy J, Elber R. Enriching the sequence substitution matrix by structural information. Proteins. 54: 41-8. PMID 14705022 DOI: 10.1002/Prot.10474  0.369
2004 Wagner M, Meller J, Elber R. Large-scale linear programming techniques for the design of protein folding potentials Mathematical Programming. 101: 301-318. DOI: 10.1007/S10107-004-0526-7  0.376
2003 Cárdenas AE, Elber R. Atomically detailed simulations of helix formation with the stochastic difference equation. Biophysical Journal. 85: 2919-39. PMID 14581195 DOI: 10.1016/S0006-3495(03)74713-4  0.349
2003 Cárdenas AE, Elber R. Kinetics of cytochrome C folding: atomically detailed simulations. Proteins. 51: 245-57. PMID 12660993 DOI: 10.1002/Prot.10349  0.434
2003 Tobi D, Elber R, Thirumalai D. The dominant interaction between peptide and urea is electrostatic in nature: a molecular dynamics simulation study. Biopolymers. 68: 359-69. PMID 12601795 DOI: 10.1002/Bip.10290  0.326
2003 Siva K, Elber R. Ion permeation through the gramicidin channel: atomically detailed modeling by the Stochastic Difference Equation. Proteins. 50: 63-80. PMID 12471600 DOI: 10.1002/Prot.10256  0.329
2002 Ghosh A, Elber R, Scheraga HA. An atomically detailed study of the folding pathways of protein A with the stochastic difference equation. Proceedings of the National Academy of Sciences of the United States of America. 99: 10394-8. PMID 12140363 DOI: 10.1073/Pnas.142288099  0.406
2002 Elber R, Ghosh A, Cárdenas A. Long time dynamics of complex systems. Accounts of Chemical Research. 35: 396-403. PMID 12069624 DOI: 10.1021/Ar010021D  0.392
2002 Meller J, Wagner M, Elber R. Maximum feasibility guideline in the design and analysis of protein folding potentials. Journal of Computational Chemistry. 23: 111-8. PMID 11913376 DOI: 10.1002/Jcc.10014  0.704
2002 Meller J, Elber R. Protein recognition by sequence-tostructure fitness: Bridging efficiency and capacity of threading models Advances in Chemical Physics. 120: 77-130. DOI: 10.1002/0471224421.Ch3  0.709
2001 Meller J, Elber R. Linear programming optimization and a double statistical filter for protein threading protocols. Proteins. 45: 241-61. PMID 11599028 DOI: 10.1002/Prot.1145  0.707
2001 Uitdehaag JC, van der Veen BA, Dijkhuizen L, Elber R, Dijkstra BW. Enzymatic circularization of a malto-octaose linear chain studied by stochastic reaction path calculations on cyclodextrin glycosyltransferase. Proteins. 43: 327-35. PMID 11288183 DOI: 10.1002/Prot.1044  0.33
2000 Tobi D, Elber R. Distance-dependent, pair potential for protein folding: results from linear optimization. Proteins. 41: 40-6. PMID 10944392 DOI: 10.1002/1097-0134(20001001)41:1<40::Aid-Prot70>3.0.Co;2-U  0.37
2000 Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD. fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science (New York, N.Y.). 289: 85-8. PMID 10884229 DOI: 10.1126/Science.289.5476.85  0.682
2000 Tobi D, Shafran G, Linial N, Elber R. On the design and analysis of protein folding potentials. Proteins. 40: 71-85. PMID 10813832 DOI: 10.1002/(Sici)1097-0134(20000701)40:1<71::Aid-Prot90>3.0.Co;2-3  0.396
2000 Zaloj V, Elber R. Parallel computations of molecular dynamics trajectories using the stochastic path approach Computer Physics Communications. 128: 118-127. DOI: 10.1016/S0010-4655(00)00038-2  0.367
2000 Mohanty D, Elber R, Thirumalai D. Probing the role of local propensity in peptide turn formation International Journal of Quantum Chemistry. 80: 1125-1128. DOI: 10.1002/1097-461X(2000)80:4/5<1125::Aid-Qua62>3.0.Co;2-J  0.373
1999 Kedem K, Chew LP, Elber R. Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories. Proteins. 37: 554-64. PMID 10651271 DOI: 10.1002/(Sici)1097-0134(19991201)37:4<554::Aid-Prot6>3.0.Co;2-1  0.376
1999 Lidar DA, Thirumalai D, Elber R, Gerber RB. Fractal analysis of protein potential energy landscapes Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 59: 2231-2243. DOI: 10.1103/Physreve.59.2231  0.581
1999 Elber R, Meller J, Olender R. Stochastic path approach to compute atomically detailed trajectories: Application to the folding of C peptide Journal of Physical Chemistry B. 103: 909-911. DOI: 10.1021/Jp983774Z  0.733
1998 Schueler-Furman O, Elber R, Margalit H. Knowledge-based structure prediction of MHC class I bound peptides: a study of 23 complexes. Folding & Design. 3: 549-64. PMID 9889166 DOI: 10.1016/S1359-0278(98)00070-4  0.306
1998 Keasar C, Tobi D, Elber R, Skolnick J. Coupling the folding of homologous proteins. Proceedings of the National Academy of Sciences of the United States of America. 95: 5880-3. PMID 9600887 DOI: 10.1073/Pnas.95.11.5880  0.402
1998 Meller J, Elber R. Computer simulations of carbon monoxide photodissociation in myoglobin: structural interpretation of the B states. Biophysical Journal. 74: 789-802. PMID 9533692 DOI: 10.1016/S0006-3495(98)74004-4  0.357
1997 Mohanty D, Elber R, Thirumalai D, Beglov D, Roux B. Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. Journal of Molecular Biology. 272: 423-42. PMID 9325101 DOI: 10.1006/Jmbi.1997.1246  0.515
1997 Keasar C, Elber R, Skolnick J. Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction. Folding & Design. 2: 247-59. PMID 9269565 DOI: 10.1016/S1359-0278(97)00033-3  0.402
1997 Gregurick SK, Fredj E, Elber R, Gerber RB. Vibrational spectroscopy of peptides and peptide-water complexes: Anharmonic coupled-mode calculations Journal of Physical Chemistry B. 101: 8595-8606. DOI: 10.1021/Jp971587F  0.577
1997 Olender R, Elber R. Yet another look at the steepest descent path Journal of Molecular Structure: Theochem. 398: 63-71. DOI: 10.1016/S0166-1280(97)00038-9  0.347
1996 Elber R. Novel methods for molecular dynamics simulations. Current Opinion in Structural Biology. 6: 232-5. PMID 8728657 DOI: 10.1016/S0959-440X(96)80080-7  0.367
1996 Olender R, Elber R. Calculation of classical trajectories with a very large time step: Formalism and numerical examples Journal of Chemical Physics. 105: 9299-9315. DOI: 10.1063/1.472727  0.366
1995 Simmerling CL, Elber R. Computer determination of peptide conformations in water: different roads to structure. Proceedings of the National Academy of Sciences of the United States of America. 92: 3190-3. PMID 7724538 DOI: 10.1073/Pnas.92.8.3190  0.376
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  0.725
1995 Elber R, Chen DP, Rojewska D, Eisenberg R. Sodium in gramicidin: an example of a permion. Biophysical Journal. 68: 906-24. PMID 7538805 DOI: 10.1016/S0006-3495(95)80267-5  0.313
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  0.608
1994 Carlson ML, Regan R, Elber R, Li H, Phillips GN, Olson JS, Gibson QH. Nitric oxide recombination to double mutants of myoglobin: role of ligand diffusion in a fluctuating heme pocket. Biochemistry. 33: 10597-606. PMID 8075059 DOI: 10.2210/Pdb1Mlu/Pdb  0.316
1994 Ulitsky A, Elber R. Application of the Locally Enhanced Sampling (LES) and a mean field with a binary collision correction (cLES) to the simulation of Ar diffusion and NO recombination in myoglobin Journal of Physical Chemistry. 98: 1034-1043. DOI: 10.1021/J100054A047  0.34
1993 Li H, Elber R, Straub JE. Molecular dynamics simulation of NO recombination to myoglobin mutants. The Journal of Biological Chemistry. 268: 17908-16. PMID 8349675  0.529
1993 Ulitsky A, Elber R. The thermal equilibrium aspects of the time dependent Hartree and the locally enhanced sampling approximations: Formal properties, a correction, and computational examples for rare gas clusters Journal of Chemical Physics. 98: 3380-3388. DOI: 10.1063/1.464110  0.327
1993 Elber R. New simulation methods for proteins and DNA Current Opinion in Structural Biology. 3: 260-264. DOI: 10.1016/S0959-440X(05)80161-7  0.366
1992 Verkhivker G, Elber R, Nowak W. Locally enhanced sampling in free energy calculations: Application of mean field approximation to accurate calculation of free energy differences The Journal of Chemical Physics. 97: 7838-7841. DOI: 10.1063/1.463456  0.351
1992 Verkhivker G, Elber R, Gibson QH. Microscopic modeling of ligand diffusion through the protein leghemoglobin: Computer simulations and experiments Journal of the American Chemical Society. 114: 7866-7878. DOI: 10.1021/Ja00046A036  0.332
1991 Czerminski R, Elber R. Computational studies of ligand diffusion in globins: I. Leghemoglobin. Proteins. 10: 70-80. PMID 2062829 DOI: 10.1002/Prot.340100107  0.315
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  0.595
1991 Choi C, Elber R. Reaction path study of helix formation in tetrapeptides: Effect of side chains The Journal of Chemical Physics. 94: 751-760. DOI: 10.1063/1.460343  0.367
1990 Rojewska D, Elber R. Molecular dynamics study of secondary structure motions in proteins: application to myohemerythrin. Proteins. 7: 265-79. PMID 2362947 DOI: 10.1002/Prot.340070308  0.389
1990 Elber R. Calculation of the potential of mean force using molecular dynamics with linear constraints: An application to a conformational transition in a solvated dipeptide The Journal of Chemical Physics. 93: 4312-4321. DOI: 10.1063/1.458713  0.401
1990 Czerminski R, Elber R. Reaction path study of conformational transitions in flexible systems: Applications to peptides The Journal of Chemical Physics. 92: 5580-5601. DOI: 10.1063/1.458491  0.348
1990 Elber R, Karplus M. Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin Journal of the American Chemical Society. 112: 9161-9175. DOI: 10.1021/Ja00181A020  0.548
1990 Czerminski R, Elber R. Self‐avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems International Journal of Quantum Chemistry. 38: 167-185. DOI: 10.1002/Qua.560382419  0.342
1989 Czerminski R, Elber R. Reaction path study of conformational transitions and helix formation in a tetrapeptide. Proceedings of the National Academy of Sciences of the United States of America. 86: 6963-7. PMID 2780552 DOI: 10.1073/Pnas.86.18.6963  0.364
1989 Yip V, Elber R. Calculations of a list of neighbors in molecular dynamics simulations Journal of Computational Chemistry. 10: 921-927. DOI: 10.1002/Jcc.540100709  0.353
1987 Elber R, Karplus M. Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science (New York, N.Y.). 235: 318-21. PMID 3798113 DOI: 10.1126/Science.3798113  0.631
1987 Karplus M, Brünger AT, Elber R, Kuriyan J. Molecular dynamics: applications to proteins. Cold Spring Harbor Symposia On Quantitative Biology. 52: 381-90. PMID 3454267 DOI: 10.1101/Sqb.1987.052.01.044  0.681
1987 Elber R, Karplus M. A method for determining reaction paths in large molecules: Application to myoglobin Chemical Physics Letters. 139: 375-380. DOI: 10.1016/0009-2614(87)80576-6  0.589
1985 Moiseyev N, Maniv T, Elber R, Gerber RB. Lifetimes of rotational resonances in molecule-surface scattering quantum versus classical results Molecular Physics. 55: 1369-1381. DOI: 10.1080/00268978500102071  0.566
1985 Elber R, Gerber RB, Kouri DJ. Multiple collision model for high energy molecular dissociation on surfaces: Effects of corrugation and of phonon participation Chemical Physics. 97: 345-356. DOI: 10.1016/0301-0104(85)87043-9  0.602
1985 Elber R, Gerber RB. Multiple-collision model for molecular dissociation in impact on solid surfaces Chemical Physics. 92: 363-379. DOI: 10.1016/0301-0104(85)85031-X  0.55
1985 Elber R, Gerber RB. Excitation of molecular rotation and of solid vibrations in high-energy collisions of I2 with MgO(100) Chemical Physics Letters. 119: 269-274. DOI: 10.1016/0009-2614(85)80415-2  0.62
1985 Kolodney E, Amirav A, Elber R, Gerber RB. Large energy transfer in hyperthermal heavy-atom-surface scattering: A study of Hg/MgO(100) Chemical Physics Letters. 113: 303-306. DOI: 10.1016/0009-2614(85)80265-7  0.6
1984 Elber R, Gerber RB. Formation of metastables and dissociative trapping in high-energy molecule-surface collisions Journal of Physical Chemistry. 88: 1571-1575. DOI: 10.1021/J150652A026  0.315
1984 Elber R. Energy scaling for model hamiltonians in molecule-surface scattering Surface Science. 141: 101-108. DOI: 10.1016/0039-6028(84)90198-5  0.312
1984 Kolodney E, Amirav A, Elber R, Gerber RB. Dissociaton and energy transfer in molecular impact on surfaces: Experimental and theoretical studies of I2/Mg(100) and I2/sapphire Surface Science. 148: 153-154. DOI: 10.1016/0039-6028(84)90040-2  0.595
1984 Gerber RB, Elber R. Centrifugal mechanism for molecular dissociation in high-energy collisions with solid surfaces Chemical Physics Letters. 107: 141-144. DOI: 10.1016/0009-2614(84)85688-2  0.627
1984 Kolodney E, Amirav A, Elber R, Gerber RB. Energy transfer and dissociation in collisions of I2 with MgO(100) Chemical Physics Letters. 111: 366-371. DOI: 10.1016/0009-2614(84)85522-0  0.624
1983 Gerber RB, Elber R. Vibrational and rotational excitation in high-energy molecule-surface collisions: Dominance of the rotational mode Chemical Physics Letters. 102: 466-470. DOI: 10.1016/0009-2614(83)87448-X  0.601
1983 Elber R, Gerber RB. Dissociation dynamics in high-energy molecule-surface collisions: The dissociation rainbow effect Chemical Physics Letters. 97: 4-8. DOI: 10.1016/0009-2614(83)87172-3  0.619
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