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

165 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 Ma P, Elber R, Makarov DE. The value of temporal information when analyzing reaction coordinates. Journal of Chemical Theory and Computation. PMID 32841001 DOI: 10.1021/acs.jctc.0c00678  0.32
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  0.76
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  0.36
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  0.36
2020 Valentine ML, Cardenas AE, Elber R, Baiz CR. Calcium-Lipid Interactions Observed with Isotope-Edited Infrared Spectroscopy. Biophysical Journal. PMID 32362342 DOI: 10.1016/j.bpj.2020.04.013  0.32
2019 Cardenas AE, Anderson CM, Webb LJ, Elber R. Partition of Positively and Negatively Charged Tryptophan Ions in Membranes with Inverted Phospholipid Heads: Simulations and Experiments. The Journal of Physical Chemistry. B. PMID 30912653 DOI: 10.1021/acs.jpcb.9b00754  0.32
2018 Anderson CM, Cardenas AE, Elber R, Webb LJ. Preferential Equilibrium Partitioning of Positively Charged Tryptophan into Phosphatidylcholine Bilayer Membranes. The Journal of Physical Chemistry. B. PMID 30481465 DOI: 10.1021/acs.jpcb.8b09872  0.32
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  0.32
2018 Valentine ML, Cardenas AE, Elber R, Baiz CR. Physiological Calcium Concentrations Slow Dynamics at the Lipid-Water Interface. Biophysical Journal. PMID 30269885 DOI: 10.1016/j.bpj.2018.08.044  0.32
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  0.32
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  0.36
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  0.32
2017 Shrestha R, Anderson CM, Cardenas AE, Elber R, Webb LJ. Direct Measurement of the Effect of Cholesterol and 6-Ketocholestanol on Membrane Dipole Field Using Vibrational Stark Effect Spectroscopy Coupled with Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 28071910 DOI: 10.1021/acs.jpcb.6b09007  0.32
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  1
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  1
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  1
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  1
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  1
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: 10.1021/acs.jpcb.5b05467  1
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  1
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  1
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  1
2015 Bello-Rivas JM, Elber R. Exact milestoning. The Journal of Chemical Physics. 142: 094102. PMID 25747056 DOI: 10.1063/1.4913399  1
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  1
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  1
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  1
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  1
2015 Elber R. From an SNP to a Disease: A Comprehensive Statistical Analysis Structure. 23: 1155. DOI: 10.1016/j.str.2015.06.005  1
2014 Cardenas AE, Elber R. Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation. The Journal of Chemical Physics. 141: 054101. PMID 25106564 DOI: 10.1063/1.4891305  1
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  1
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  1
2014 Elber R, Cardenas AE. Molecular dynamics at extended timescales Israel Journal of Chemistry. DOI: 10.1002/ijch.201400015  1
2013 Cardenas AE, Elber R. Computational study of peptide permeation through membrane: Searching for hidden slow variables. Molecular Physics. 111: 3565-3578. PMID 26203198  0.32
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  1
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  1
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  1
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  1
2013 Elber R, Kirmizialtin S. Molecular machines. Current Opinion in Structural Biology. 23: 206-11. PMID 23305848 DOI: 10.1016/j.sbi.2012.12.002  1
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  1
2013 Cardenas AE, Elber R. Computational study of peptide permeation through membrane: Searching for hidden slow variables Molecular Physics. 111: 3565-3578. DOI: 10.1080/00268976.2013.842010  1
2013 Di Pierro M, Elber R. Automated optimization of potential parameters Journal of Chemical Theory and Computation. 9: 3311-3320. DOI: 10.1021/ct400313n  1
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  1
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  1
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  1
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  1
2012 Kirmizialtin S, Silalahi AR, Elber R, Fenley MO. The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations. Biophysical Journal. 102: 829-38. PMID 22385854 DOI: 10.1016/j.bpj.2011.12.055  1
2012 Kirmizialtin S, Pabit SA, Meisburger SP, Pollack L, Elber R. RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations. Biophysical Journal. 102: 819-28. PMID 22385853 DOI: 10.1016/j.bpj.2012.01.013  1
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  1
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  1
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  1
2012 Burke S, Elber R. Super folds, networks, and barriers. Proteins. 80: 463-70. PMID 22095563 DOI: 10.1002/prot.23212  1
2012 Elber R, Cardenas AE. Coarse-grained methods: Theory Comprehensive Biophysics. 9: 2-26. DOI: 10.1016/B978-0-12-374920-8.00902-4  1
2012 Cardenas AE, Elber R. Enhancing the capacity of molecular dynamics simulations with trajectory fragments Rsc Biomolecular Sciences. 1: 117-137.  1
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  1
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  1
2011 Elber R. Progress at last. Structure (London, England : 1993). 19: 1725. PMID 22153491 DOI: 10.1016/j.str.2011.11.005  1
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  1
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  1
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  1
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  1
2010 Kirmizialtin S, Elber R. Computational exploration of mobile ion distributions around RNA duplex. The Journal of Physical Chemistry. B. 114: 8207-20. PMID 20518549 DOI: 10.1021/jp911992t  1
2010 Elber R. Watching biomolecular machines in action. Structure (London, England : 1993). 18: 415-6. PMID 20399177 DOI: 10.1016/j.str.2010.03.002  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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: 484-494. DOI: 10.1021/ct060028m  1
2006 Elber R. Calculation of classical trajectories with boundary value formulation Lecture Notes in Physics. 703: 435-451. DOI: 10.1007/3-540-35273-2_12  1
2006 Leimkuhler B, Chipot C, Elber R, Laaksonen A, Mark A, Schlick T, Schütte C, Skeel R. New Algorithms for Macromolecular Simulation Lecture Notes in Computational Science and Engineering. 49.  1
2006 Joachims T, Galor T, Elber R. Learning to Align Sequences: A Maximum-Margin Approach Lecture Notes in Computational Science and Engineering. 49: 58-69.  1
2006 Scheraga HA, Liwo A, Oldziej S, Czaplewski C, Pillardy J, Lee J, Ripoll DR, Vila JA, Kazmierkiewicz R, Saunders JA, Arnautova YA, Gibson KD, Jagielska A, Khalili M, Chinchio M, ... ... Elber R, et al. The Protein Folding Problem Lecture Notes in Computational Science and Engineering. 49: 90-100.  1
2006 Leimkuhler B, Chipot C, Elber R, Laaksonen A, Mark A, Schlick T, Schütte C, Skeel R. Preface Lecture Notes in Computational Science and Engineering. 49: V-VII.  1
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  1
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  1
2005 Weinbach Y, Elber R. Revisiting and parallelizing SHAKE Journal of Computational Physics. 209: 193-206. DOI: 10.1016/j.jcp.2005.03.015  1
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  1
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  1
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  1
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  1
2004 Meyerguz L, Kempe D, Kleinberg J, Elber R. The evolutionary capacity of protein structures Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 8: 290-297.  1
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  1
2003 Cárdenas AE, Elber R. Kinetics of cytochrome C folding: atomically detailed simulations. Proteins. 51: 245-57. PMID 12660993 DOI: 10.1002/prot.10349  1
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  1
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  1
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  1
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  1
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  1
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.  1
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  1
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  1
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  1
2000 Elber R, Frank A, Almog J. Chemical development of latent fingerprints: computational design of ninhydrin analogues. Journal of Forensic Sciences. 45: 757-60. PMID 10914567  1
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  1
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  1
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  1
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.  1
2000 Elber R, Shalloway D. Temperature dependent reaction coordinates Journal of Chemical Physics. 112: 5539-5545.  1
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  1
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.  1
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.  1
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  1
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  1
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  1
1998 Teo BK, Strizhev A, Elber R, Zhang H. Iconography of Icosahedra. Calculations of Metallic Energies and Relative Stabilities of Stereoisomers of Binary Icosahedral Clusters Inorganic Chemistry. 37: 2482-2495.  1
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  1
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  1
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  1
1997 Olender R, Elber R. Yet another look at the steepest descent path Journal of Molecular Structure: Theochem. 398: 63-71.  1
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  1
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.  1
1995 Quillin ML, Li T, Olson JS, Phillips GN, Dou Y, Ikeda-Saito M, Regan R, Carlson M, Gibson QH, Li H. Structural and functional effects of apolar mutations of the distal valine in myoglobin. Journal of Molecular Biology. 245: 416-36. PMID 7837273 DOI: 10.1006/jmbi.1994.0034  1
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  1
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  1
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  1
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  1
1995 Keasar C, Elber R. Homology as a tool in optimization problems: Structure determination of 2D heteropolymers Journal of Physical Chemistry. 99: 11550-11556.  1
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.  1
1994 Simmerlin C, Elber R. Hydrophobic "collapse" in a cyclic hexapeptide: Computer simulations of CHDLFC and CAAAAC in water Journal of the American Chemical Society. 116: 2534-2547.  1
1993 Chiancone E, Elber R, Royer WE, Regan R, Gibson QH. Ligand binding and conformation change in the dimeric hemoglobin of the clam Scapharca inaequivalvis. The Journal of Biological Chemistry. 268: 5711-8. PMID 8449933  1
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  1
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  1
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.  1
1992 Gibson QH, Regan R, Elber R, Olson JS, Carver TE. Distal pocket residues affect picosecond ligand recombination in myoglobin. An experimental and molecular dynamics study of position 29 mutants. The Journal of Biological Chemistry. 267: 22022-34. PMID 1429552  1
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.  1
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.  1
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  1
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 The Journal of Chemical Physics. 95: 9277-9287.  1
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.  1
1991 Nowak W, Czerminski R, Elber R. Reaction path study of ligand diffusion in proteins: Application of the self penalty walk (SPW) method to calculate reaction coordinates for the motion of CO through leghemoglobin Journal of the American Chemical Society. 113: 5627-5637.  1
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  1
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.  1
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.  1
1990 Ulitsky A, Elber R. A new technique to calculate steepest descent paths in flexible polyatomic systems The Journal of Chemical Physics. 92: 1510-1511.  1
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.  1
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  1
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  1
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  1
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  1
1986 Elber R, Karplus M. Low-frequency modes in proteins: Use of the effective-medium approximation to interpret the fractal dimension observed in electron-spin relaxation measurements. Physical Review Letters. 56: 394-397. PMID 10033176 DOI: 10.1103/PhysRevLett.56.394  1
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  1
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  1
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  1
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  1
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  1
1985 Elber R. Comment on reactive diatom-solid surface collision: A quantum mechanical approach The Journal of Chemical Physics. 83: 6544-6545.  1
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  1
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  1
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  1
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  1
1984 Elber R, Gerber RB. Formation of metastables and dissociative trapping in high-energy molecule-surface collisions Journal of Physical Chemistry. 88: 1571-1575.  1
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  1
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  1
1983 Elber R, Gerber RB. Multiple-collision rotational rainbow effect in molecule-surface scattering The Journal of Chemical Physics. 79: 4087-4088.  1
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