LIST OF PUBLICATIONS (e-copy available upon request from ron@ices.utexas.edu)                                                                   within the group only

108 Leonid Meyerguz, Jon Kleinberg, and Ron Elber, "The network of sequence flow between protein structures", Proc. Natl. Acad. Sci. USA, (2007),104,11627-11623

107 Michal Z Steinberg, Kathrin Breuker, Ron Elber and R. Benny Gerber, "The dynamics of water evaporation from partially solvated cytochrome c in the gas phase", Physical Chemistry and Chemical Physics, (2007),9,4690-4697.

106 Chun-Nam John Yu, Thorsten Joachims, Ron Elber and Jaroslaw Pillardy, "Support Vector Training of Protein Alignment Models", RECOMB 2007, accepted.

105 Ron Elber, "A milestoning study of the kinetics of an allosteric transition: Atomically detailed simulations of deoxy Scapharca hemoglobin", Biophysical J. ,2007 92: L85-L87

104 Anthony M.A. West, Ron Elber, and David Shalloway, "Extending molecular dynamics timescales with milestoning: Example of complex kinetics in a solvated peptide", J. Chem. Phys. (2007),126,145104

103 Ron Elber, "Calculations of classical trajectories with boundary value formulation", Lecture Notes in Physics, 703, 435-451(2006)

102 Chun-Num John Yu, Thorsten Joachim, and Ron Elber "Training protein threading models using structural SVMs", ICML 2006

101 Dov Bai and Ron Elber, "Calculation of point-to-point short time and rare trajectories with boundary value formulation", J. Chemical Theory and Computation, 2,484-494(2006)

100 Jian Qiu and Ron Elber, "SSALN: An alignment algorithm using structure-dependent substitution matrices and gap penalties learned from structurally aligned protein pairs", Proteins, Structure, Function and Bioinformatics, 62,881-891(2006)

99 Thorsten Joachims, Tamara Galor, and Ron Elber, "Learning to Align Sequences: A Maximum-Margin approach", pp. 57-58, in Springer Verlag Notes in Computational Science and Engineering Vol. 49 "New Algorithms for macromolecular modeling" Ed Ben Leimkuhler, 2005.

98 Yael Weinbach and Ron Elber, "Revisiting and Parallelizing SHAKE", Journal of Computational Physics, 209:193-206(2005)

97 Jian Qiu and Ron Elber, "Atomically detailed potentials to recognize native and approximate protein structures", Proteins, Structure, Function, and Bioinformatics, 61:44-55,2005

96 Ron Elber, "Long-timescale simulation methods", Current opinion in Structural Biology, 15:151-156(2005)

95 Ron Elber, Jian Qiu, Leonid Meyerguz, and Jon Kleinberg, "Sequence-structure relationships in proteins:", a chapter in "Soft Condensed Matter Physics in Molecular and Cell Biology", Edited by W C K Poon and D Andelman,  Taylor Francis group. New York, London, 2006

94 Anton K. Faradjian and Ron Elber, "Computing time scales from reaction coordinates by milestoning", J. Chem. Phys. 120:10880-10889(2004)

93 Leonid Meyerguz, David Kempe, Jon Kleinberg, and Ron Elber, “The evolutionary capacity of protein structures”. RECOMB 04,

92 Leonid Meyerguz, Catherine Grasso, Jon Kleinberg, and Ron Elber, “Computational analysis of sequence selection mechanisms”, Structure, 12,547-557(2004)

91 Alfredo Cárdenas and Ron Elber, "Atomically detailed simulations of helix 
formation with the stochastic difference equation", Biophysical Journal,(2003),85,2919-2939

90 Octavian Teodorescu, Tamara Galor, Jaroslaw Pillardy, and Ron Elber, 
"Enriching the sequence substitution matrix by structural information", 
Proteins, Structure, Function and Genetics, (2004),54,41-48

89 Alfredo Cárdenas and Ron Elber, "Kinetics of Cytochrome C Folding: 
Atomically Detailed Simulations", Proteins, Structure Function and 
Genetics, 51,245-257(2003)

88 Michael Wagner, Jaroslaw Meller, and Ron Elber, "Large-scale linear 
programming techniques for the design of protein folding potentials", 
Mathematical Programming, (2004),101,301-318

87 Dror Tobi, Devarajan Thirumalai, and Ron Elber, "The dominant interaction 
between peptide and urea is electrostatic in nature: A molecular 
dynamics simulation study", Biopolymers 68,359-369(2003)

86 Koneshan Siva and Ron Elber, "Ion Permeation Through the Gramicidin 
Channel: Atomically Detailed Modeling by the Stochastic Difference 
Equation", Proteins Structure Function and Genetics, 50,63-80(2003)

85 Ron Elber, Avijit Ghosh and Alfredo Cárdenas, "The Stochastic Difference 
Equation as a tool to compute long time dynamics", a chapter in 
"Bridging the time scale gap", Editors: Peter Nielaba, Michel Mareschal 
and Giovanni Ciccotti, Springer Verlag, Berlin, 2002, pp 335-363

84 Avijit Ghosh, Ron Elber, and Harold Scheraga, "An atomically detailed 
study of the folding pathways of Protein A with the Stochastic 
Difference Equation", Proc. Natl. Acad. Sci., 99,10394-10398(2002).

83 Ron Elber, Avijit Ghosh, Alfredo Cárdenas and Harry Stern, "Bridging the 
gap between reaction pathways, long time dynamics and calculation of 
rates", Advances in Chemical Physics, 126,93-129(2003)

82 Jaroslaw Meller, Michael Wagner and Ron Elber, "Maximum Feasibility 
Guideline in the Design and Analysis of Protein Folding Potentials", J. 
of Computational Chemistry, 23,111-118(2002).

81 Ron Elber, Avijit Ghosh and Alfredo Cárdenas, "Long time dynamics of 
complex systems", Account of Chemical Research, 35,396-403(2002)

80 Jaroslaw Meller and Ron Elber, "Linear Optimization and a double 
Statistical Filter for protein threading protocols", Proteins, Structure, 
Function and Genetics, 45,241-261(2001)

79 Jaroslaw Meller and Ron Elber, 2002, "Protein recognition by sequence-to-
structure fitness: Bridging efficiency and capacity of threading models", 
Advances in Chemical Physics, Volume 120. Editor, Richard Friesner, 
pp. 77-130

78 Joost C.M. Uitdehaag, Bart A. van der Veen, Lubbert Dijkhuizen, Ron Elber 
and Bauke W. Dijkstra, "The enzymatic circularization of a malto-
octaose linear chain studied by stochastic reaction path calculations on 
cyclodextrin glycosyltransferase", Proteins, Structure Function and 
Genetics, 327-335,43(2001).

77 D. Mohanty, R. Elber, and D. Thirumalai, "Probing the role of the local 
propensity in peptide turn formation", International Journal of Quantum 
Chemistry, 80, 1125-1128 (2000).

76 Dror Tobi and Ron Elber, "Distance dependent, pair potential for protein 
folding: Results from linear optimization", Proteins, Structure Function 
and Genetics, 41, 40-16 (2000).

75 Anne Frary, Clint Nesbitt, Amy Frary, Silvana Grandillo, Esther van der 
Knaap, Bin Cong, Jiping Liu, Jaroslaw Meller, Ron Elber, Kevin B. 
Alpert, Steven D. Tanksley, "Cloning, Transgenic Expression and 
Function of fw2.2: a Quantitative Trait Locus Key to the Evolution of 
Tomato Fruit", Science, 289, 85-88 (2000).

74 Ron Elber, Arie Frank and Joseph Almog, "Chemical Development of 
Latent Fingerprints: Computational Design of Ninhydrin Analogues", J. 
Forensic Sci. 745-748, 45 (2000).

73 Ron Elber and David Shalloway, "Temperature dependent reaction 
coordinates", J. Chem. Phys. 112, 5539-5545 (2000).

72 Veaceslav Zaloj and Ron Elber, "Parallel Computations of Molecular 
Dynamics Trajectories Using Stochastic Path Approach", Computer 
Physics Communication, 128, 118-127 (2000).

71 Dror Tobi, Gil Shafran, Nathan Linial and Ron Elber, "On the design and 
analysis of protein folding potentials", "Proteins, Structure Function and 
Genetics", 40, 71-85 (2000).

70 Klara Kedem, L. Paul Chew and Ron Elber, "Unit Vector RMS (URMS) as 
a Tool to Analyze Molecular Dynamics Trajectories", "Proteins, 
Structure Function and Genetics", 37, 554-564 (1999).

69 R. Elber and M. Karplus, "Reply to the paper by Stacho et al. "On the Elber-
Karplus Reaction Path-Following Method and Related Procedures", 
Chem. Phys. Lett. 311, 335-340 (1999).

68 R. Elber, J. Meller and R. Olender, "A stochastic path approach to compute 
atomically detailed trajectories: Application to the folding of C peptide", 
J. Phys. Chem. B, 103, 899-911 (1999).

67 D. A. Lidar, D. Thirumalai, R. Elber, R. B. Gerber, "Fractal Analysis of 
Protein Potential Energy Landscapes", Phys. Rev. E, 59, 2231-2243 
(1999).

66 O. Schueler-Furman, Ron Elber and Hanah Margalit, "Knowledge-based 
structure prediction of MHC class I bound peptides: A study of twenty-
three complexes", Folding and Design, 3, 549-564 (1998).

65 R. Elber, D. Mohanty, and C. Simmerling, "Dynamics of peptide folding", 
in "Classical and Quantum Dynamics in Condensed Phase Simulations", 
pp. 423-444, Ed. B. Berne, G. Ciccotti, and D. Coker, World Scientific, 
Singapore, 1998.

64 R. Elber, B. Roux, and R. Olender, "Application of a stochastic path integral 
to the computations of an optimal path and ensembles of trajectories", in 
"Lecture Notes in Computational Science and Engineering", Ed. P. 
Deuflhard, J. Hermans, B. Leimukhlar, A. E. Mark, S. Reich, R. D. 
Skeel, Volume 4, "Computational Molecular Dynamics: Challenges, 
Methods, Ideas", Springer Verlag, Berlin Heidelberg, 1999, pp. 263-280.

63 Teo, Boon K.; Strizhev, Alex; Elber, Ron; Zhang, Hong, "Iconography of 
Icosahedra. Calculations of Metallic Energies and Relative Stabilities of 
Stereoisomers of Binary Icosahedral Clusters", Inorg. Chem., 37, 2482-
2495 (1998).

62 C. Keasar, D. Tobi, R. Elber and J. Skolnick, "Coupling the folding of 
homologous proteins", Proc. Natl. Acad. Sci. USA, 95, 5880-5883 
(1998).

61 J. Meller and R. Elber, "Computer Simulations of Carbon Monoxide Photo-
dissociation in Myoglobin: Structural Interpretation of the B states" 
Biophys. J. 74, 789-802 (1998).

60 S. K. Gregurick, E. Fredj, R. Elber and R.B. Gerber, "Vibrational 
spectroscopy of peptides and peptide water complexes: Anharmonic 
coupled mode calculations", J. Phys. Chem.-B 42, 8595-8606 (1997).

59 D. Mohanty, R. Elber, Devarajan Thirumalai, Dimitrii Beglov and Benoit 
Roux, "Kinetics of peptide folding: Computer simulations of SYPFDV 
and peptide variants in water", J. Mol. Biol., 272, 423-442 (1997).

58 C. Keasar, R. Elber and J. Skolnick, "Simultaneous and coupled energy 
optimization of homologous proteins: A new tool for structure 
prediction", Folding and Design, 2, 247-259 (1997).

57 R. Olender and R. Elber, "Yet another look at the steepest descent path", J. 
Mol. Struct. Theochem and the proceeding of the WATOC symposium, 
398-399, 63-72 (1997).

56 R. Elber, editor, a monograph on "Recent developments in theoretical 
studies of proteins", World Scientific, 1996, and a chapter, "Reaction 
path studies of biomolecules".

55 R. Olender and R. Elber, "Calculation of classical trajectories with a very 
large time step: Formalism and numerical examples", J. Chem. Phys., 
105, 9299-9315 (1996).

54 R. Elber, "Novel methods for molecular dynamics simulations", an invited 
review for Current Opinion in Structural Biology ?, 6, 232-235 (1996).

53 C. Keasar and R. Elber, "Homology as a tool in optimization problems: 
Structure determination of 2D heteropolymers", J. Phys. Chem., 99, 
11550-11556 (1995).

52 A. Roitberg, R.B. Gerber, R. Elber and M.A. Ratner, "Anharmonic 
wavefunctions of proteins: Quantum self-consistent field calculations of 
BPTI", Science, 268, 1319-1322 (1995).

51 C. Simmerling and R. Elber, "Computer determination of peptide 
conformations in water: Different roads to structure", Proc. Natl. Acad. 
Sci. USA, 92, 3190-3193 (1995).

50 R. Elber, A. Roitberg, C. Simmerling, R. Goldstein, H. Li, G. Verkhivker, 
C. Keasar, J. Zhang and A. Ulitsky "MOIL: A program for simulations 
of macromolecules", Computer Physics Communications, 91, 159-
189(1995).

49 M.L. Quillin, T. Li, J.S. Olson, G.N. Phillips, Y. Dou, M. Ikeda-Saito, R. Regan,
M. Carlson, Q. H. Gibson, H. Li and R. 
Elber, "Structural and functional effects of apolar mutations of 
the distal valine in myoglobin", J. Mol. Biol., 245,416-436(1995)

48 C. Simmerling, R. Elber and J. Zhang, "Moil-View - a program for 
visualization of structure and dynamics of biomolecules and STO - a 
program for computing stochastic paths", in "The biochemistry", 
Modeling of Biomolecular Structures and Mechanisms, 1995, Ed. A. 
Pullman et al, 241-265, 1995 (Kluwer Academic Publishers, 
Netherlands) 

47 M.L. Carlson, R. Regan, R. Elber, H. Li, G.N. Phillips Jr., J.S. Olson and 
Q.H. Gibson, "Nitric oxide recombination to double mutants of 
myoglobin: The role of ligand diffusion in a fluctuating heme pocket", 
Biochemistry, 33, 10597-10606 (1994).

46 R. Elber, D. Chen, D. Rojewska and R.S. Eisenberg, "Sodium in gramicidin: 
An example of a permion", Biophys. J., 68, 906-924 (1995).

45 C. Simmerling and R. Elber, "Hydrophobic "collapse" in a cyclic 
hexapeptide: Computer simulations of CHDLFC and CAAAAC in 
water", J. Amer. Chem. Soc. 116, 2534 (1994).

44 A. Ulitsky and R. Elber, "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", J. 
Phys. Chem., 98, 1034-1043 (1994).

43 A. Roitberg and R. Elber, " The Locally Enhanced Sampling for Side Chain 
Modeling", an invited chapter to "The protein folding problem and 
tertiary structure prediction" Ed., K.M. Merz and S.M. LeGrand, 
Birkhauser Boston, pp 1-42, (1994).

42 Ron Elber, Adrian Roitberg, Carlos Simmerling, Gennady Verkhivker, 
Robert Goldstein, Alex Ulitsky and Haiying Li, "MOIL: A molecular 
dynamics program with emphasis on conformational searches and 
reaction path calculations in large biological molecules", NATO 
conference proceeding on "Statistical Mechanics and Protein Structure", 
Cargese, June 1994, Plenum press, Ed. S. Doniach, pp. 165-191.

41 H. Li, R. Elber and J.E. Straub, "Molecular Dynamics Simulations of NO 
Recombination to Myoglobin Mutants", J. Biol. Chem. 268, 17908 
(1993).

40 E. Chiancone, R. Elber, W.E. Royer Jr., R. Regan and Q.H. Gibson "Ligand 
binding and conformational change in the dimeric hemoglobin of the 
clan scapharca inaequivalvis", J. Biol. Chem. 268, 5711 (1993).

39 Quentin H. Gibson, Rebecca Regan, Ron Elber, John S. Olson and Theodore 
E. Carver, "Distal Pocket Residues Affect Picosecond Recombination in 
Myoglobin: An experimental and Molecular Dynamics Study of Position 
29 Mutants", J. Biol. Chem. 267, 22022 (1992).

38 Ron Elber, "New Simulation Methods for Proteins and Nucleic Acids", an 
invited review for "Current Opinion in Structural Biology", 3, 260 
(1993).

37 A. Ulitsky and R. Elber, " The equilibrium of the time dependent Hartree 
and the Locally Enhanced Sampling approximations: Formal properties, 
corrections, and computational studies of rare gas clusters", J. Chem. 
Phys., 98, 3380 (1993).

36 G. Verkhivker, R. Elber and W. Nowak, "Locally Enhanced Sampling in 
Free Energy Calculations: Application of Mean Field Approximation to 
Accurate Calculations of Free Energy Differences", J. Chem. Phys., 97, 
7838 (1992).

35 G. Verkhivker, Ron Elber and Quentin H. Gibson, "Microscopic modeling 
of ligand diffusion through the protein leghemoglobin: Computer 
simulations and experiments", J. Amer. Chem. Soc, 114, 7866 (1992).

34 A. Roitberg and R. Elber, "Modeling side chains in peptides and proteins: 
Application of the Locally Enhanced Sampling (LES) and the simulated 
annealing methods to find minimum energy conformations", J. Chem. 
Phys. 95, 9277 (1991). 

33 R. Czerminski, A. Roitberg, C. Choi, A. Ulitsky and R. Elber, 
"Conformational Transitions", A contributed manuscript for the 
proceeding of the conference "Advances in Biomolecular Simulations", 
AIP Conference Proceeding 239, Ed. R. Lavery, J.L. Rivail and J. Smith, 
AIP 1991.

32 W. Nowak, R. Czerminski and R. Elber, "Reaction path study of ligand 
diffusion in proteins: Application of the SPW method to calculate 
reaction coordinate for the motion of CO through leghemoglobin", J. 
Amer. Chem. Soc., 113, 5627 (1991).

31 C. Choi and R. Elber, "Reaction path study of helix formation in 
tetrapeptides: Effect of side chains ", J. Chem. Phys, 751, 94 (1991).
30 R. Elber, Ryszard Czerminski, Wieslaw Nowak, Chyung Choi, and Alex 
Ulitksy, an invited review "Dynamics of Conformational Transitions and 
Diffusion in Proteins", in "Chemical Design and Automation News", 5, 
12 (1990).

29 R. Elber and M. Karplus, "Enhanced sampling in molecular dynamics: Use 
of the Time-Dependent Hartree approximation for a simulation of 
carbon monoxide diffusion through myoglobin", J. Amer. Chem. Soc., 
112, 9161 (1990).

28 R. Elber, "Calculation of the potential of mean force using molecular 
dynamics with linear constraints: An application to a conformational 
transition of a solvated dipeptide", J. Chem. Phys. 93, 4312 (1990).

27 R. Czerminski and R. Elber, "Computational studies of ligand diffusion in 
globins: I. leghemoglobin", "Proteins" 10, 70 (1991).

26 R. Czerminski and R. Elber, "Self avoiding walk between two fixed points 
as a tool to calculate reaction paths in large molecular systems", Int. J. 
Quant. Chem. 24, 167-186 (1990) and The Proc. of Sanibel Symposia 
1990.

25 R. Czerminski and R. Elber, "Reaction path study of conformational 
transitions in flexible systems: Applications to peptides" J. Chem. Phys. 
92, 5580 (1990).

24 A. Ulitsky and R. Elber, "A new technique to calculate steepest descent 
paths in flexible polyatomic systems", J. Chem. Phys. 96, 1510 (1990).

23 D. Rojewska and R. Elber, "Molecular dynamics of secondary structure 
motions in proteins: Application to myohemerythrin.", Proteins, 7, 265 
(1990).

22 M. Karplus, R. Elber, J. Gao, K. Kuzcera, B. Tidor, "Simulations of 
Proteins" In "Highlights of Modern Biochemistry", Kotyk, A.; Skoda J.; 
Paces V. and Kostka V. Eds.; VSP International Science Publishers: 
Zeist, Czechoslovakia, pp 3-10, (1989). 

21 R. Czerminski and R. Elber, "Reaction path study of conformational 
transitions and helix formation in a tetrapeptide" Proc. Natl. Acad. Sci., 
86, 6963 (1989).

20 V. Yip and R. Elber, "Calculations of a list of neighbors in molecular 
dynamics simulations", J. Comput. Chem., 10, 921 (1989).

19 R. Elber, "Fractal Analysis of Proteins" a chapter in "The fractal approach to 
heterogeneous chemistry", Ed. David Avnir, John Wiley & Sons 1989.

18 M. Karplus, A.T. Brunger, R. Elber and J. Kuriyan, "Molecular dynamics: 
Application to proteins", A chapter in "Structure and expression, from 
proteins to ribosomes" Vol. 1 Edited by M.H. Sarma and R.H. Sarma, 
Adenine Press 1988.

17 R. Elber and M. Karplus, "A method for determining reaction paths in large 
molecules: Application to myoglobin" Chem. Phys. Lett. 139, 375 
(1987).

16 M. Karplus, A.T. Brunger, R. Elber and J. Kuriyan, "Molecular dynamics : 
Applications to proteins" Cold Spring Harbor Symposium, 1987.

15 R. Elber and M. Karplus, "Multiple conformational states of proteins : A 
molecular dynamics analysis of myoglobin" Science 235, 318 (1987).

14 R. Elber and M. Karplus, "Low frequency modes of proteins: Interpretation 
of the fractal dimension observed in paramagnetic relaxation 
experiments by effective medium calculations" Phys. Rev. Lett. 56, 394 
(1986).

13 R. Elber, "Comment on Reactive diatom-solid surface collision: A quantum 
mechanical approach" J. Chem. Phys. 83, 6544 (1985).

12 N. Moiseyev, T. Maniv, R. Elber and R.B. Gerber, "Lifetimes of rotational 
resonances in molecule-surface scattering : quantum versus classical 
results" Mol. Phys. 55, 1369 (1985).

11 R. Elber and R.B. Gerber, "Excitation of molecular rotation and of solid 
vibrations in high energy collisions of I2 with MgO(100)" Chem. Phys. 
Lett. 119, 269 (1985).

10 R. Elber, R.B. Gerber and D.J. Kouri, "Multiple collision model for high-
energy molecular dissociation on surfaces : Effects of corrugation and of 
phonon participation" Chem. Phys. 97, 345-363 (1985) .

9 R. Elber and R.B. Gerber, "Multiple collision model for molecular 
dissociation in impact on solid surfaces", Chem. Phys. 92, 363 (1985).

8 R. Elber, "Energy scaling for model hamiltonians in molecule-surface 
scattering" Surface Sci. 141, 101 (1984). 

7 E. Kolodney, A. Amirav, R. Elber and R.B. Gerber, "Energy transfer and 
dissociation in collisions of iodine molecule with MgO(100)" Chem. 
Phys. Lett. 111, 366 (1984).

6 E. Kolodney, A. Amirav, R. Elber and R.B. Gerber, "Large energy transfer 
in hyperthermal heavy atom-surface scattering : A study of 
Hg/MgO(100)", Chem. Phys. Lett. 113, 303 (1984).

5 R.B. Gerber and R. Elber, "Centrifugal mechanism for molecular 
dissociation in high energy collisions with solid surfaces" Chem. Phys. 
Lett. 107, 141 (1984).

4 R. Elber and R.B. Gerber, "Formation of metastables and dissociative 
trapping in high energy molecule-Surface collisions" J. Phys. Chem. 88, 
1571 (1984).

3 R.B. Gerber and R. Elber, "Molecular excitation in high energy collisions 
with solid surfaces: The dominance of the rotational mode" Chem. Phys. 
Lett. 102, 466 (1983).

2 R. Elber and R.B. Gerber, "Multiple collision rotational rainbow effect in 
molecule surface scattering" J. Chem. Phys. 79, 4987 (1983). 

1 R. Elber and R.B. Gerber, "Dissociation dynamics in high-energy molecule-
surface collisions: The dissociation Rainbow Effect" Chem.. Phys. Lett. 
97, 4 (1983).