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Bibliography

General Bibiliography

Note: This list was generated by an automated conversion of our bibliogrpahic databases and other sources. It is presently unsufficiently checked for accuracy, please excuse many errors and formating mistakes. Please report errors here.

AC93
H. Ammar and Y. Cherruault, Approximation of a several variables function by a one variable function and application to global optimization, Mathl. Comput. Modelling 18 (1993), no. 2, 17-21.
AGS67
Harry M. Schey, Abraham Goldberg and Judah L. Schwartz, Computer-generated motion pitures of one-dimensional quantum-mechanical transmission and reflection phenomena, Am. J. Phys. 135 (1967), no. 3, 177-186.
AM91
Martin Karplus and Christopher M. Dobson Andrew Miranker, Sheena E. Radford, Demonstration by nmr of folding domains in lysozyme, Nature 349 (1991), 633-636.
AM95a
F. Avbelj and J. Moult, Proteins 23 (1995), 129-141.
AM95b
to3em, Proteins: SF&G 23 (1995), 129.
AM95c
Franc Avbelj and John Moult, Role of eloctrostatic screening in determining protein main chain conformational preferences, Biochemistry 34 (1995), 755-764.
And92
Christopher R. Anderson, An implementation of the fast multipole methodwithoutmultipoles, SIAM J. Sci. Stat. Comput. 13 (1992), no. 4, 923-947.
Anf73a
C. B. Anfinsen, Science 181 (1973), 223-230.
Anf73b
C.B. Anfinsen, Science 181 (1973), 223-230.
App85
Andrew W. Appel, An efficient program for many-body simulation, SIAM J. Sci. Stat. Comput. 6 (1985), no. 1, 85-103.
APPZ85
F. Aluffi-Pentini, V. Parisi, and F. Zirilli, Global optimization and stochastic differentialequations, J. Optim. Theory Appl. 47 (1985), no. 1, 1-16.
AT94
R. Abagyan and M. Totrov, Biased probability monte carlo conformation searches and electrostatic calculations for peptides and proteins, J. Molec. Biol. 235 (1994), 983-1002.
Avb92
F. Avbelj, Use of a potential of mean force to analyze free energy contributions in protein folding, Biochemistry 31 (1992), 6290-6297.
AvM94
Eugene Shakhnovich Andrej Šali and MartinKarplus, How does a protein fold ?, Nature 369 (1994), 248-251.
aWvG96
F. Fraternali ans W.F. van Gunsteren, An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution, J. Mol. Biol. 256 (1996), 939.
AZ98
G. Abramson and D. H. Zanette, Globally coupled maps with asynchronous updating, cond-mat/980515 (1998).
BA74
S. Brehmer and H. Apelt, Analysis ii, VEB Deutscher Verlag der Wissenschaften, Berlin, 1974.
BAK03
B. Bothner, Y. Aubin, and R. W. Kriwacki, Peptides derived from two dynamically disordered proteins self-assemble into amyloid-like fibrils, J. Am. Chem. Soc. 125 (2003), 3200.
Bal94
Robert L. Baldwin, Matching speed and stability, Nature 369 (1994), 183-184.
BBaA99
J. Brooke, D. Bitko, and T.F. Rosenbaum andG. Aeppli, Science 284 (1999), 779.
BBSaK83
B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, and S. Swaminathan and M. Karplus, CHARMM: A program for macromolecular energy, minimization, and dynamics calculations, J. Comp. Chem. 4 (1983), no. 2, 187-217.
BCH85
G. F. M. Beenker, T. Claasen, and P. W. C. Hermes, Philips J. Res. 40 (1985), 289.
BDW68
M. Bass, T.F. Deutsch, and M.J. Weber, Frequency- and time-dependent gain characteristicsoflaser- and flashlamp-pumped dye solution lasers, App. Phys. Lett. 13 (1968), no. 4, 120-126.
BE98
R. D. Baumeister and S. Eimer, Angew. Chemie (Intl. Ed.) 37 (1998), 2978.
Bel70
Horst Belkner, Matrizen, 5. ed., Teubner Verlag, Stuttgart, 1970.
Ber87
J. Bernasconi, J. Physique 48 (1987), 559.
Ber92
B.A. Berg, Int. J. Mod. Phys. C3 (1992), 1083.
BFMK82
J.T. Bolin, D.J. Filman, A. Matthews, and R.C. Hamlinand J. Kraut, Crystal structures of escherichia coli and lactobacilluscasei dihydrofolate reductase refined at 1.7å resolution, J. Biol. Chem. 257 (1982), 13650.
BFPN97
Uga Bastolla, Helge Frauenkorn, Erwin Gerstnerand PeterGrassberger, and Walter Nadler, Testing a new monte carlo algorithm for proteinfolding, cond-mat/9710030 (1997).
BFR00
C. Bissantz, G. Folkerts, and D. Rognan, Protein-based virtual screening of chemical databases.1. evaluation of different docking/scoring combinations, J. Med. Chem. 43 (2000), 4759.
BG84
Rudolf Brauner and Fritz Geiß, Das abitur-wissen mathematik, 7. ed., Fischer Taschenbuch Verlag, Frankfurt a.M., 1984.
BGaR88
F. Barahona, M. Grötschel, and M. Juenger andG. Reinelt, Operations Research 36 (1988), 493.
BHW92a
Burg, Haf, and Wille, H"ohere mathematik f"ur ingenieure band i analysis, 3. ed., Teubner Verlag, Stuttgart, 1992.
BHW92b
to3em, H"ohere mathematik f"ur ingenieure band iilinearealgebra, 3. ed., Teubner Verlag, Stuttgart, 1992.
BHW93
to3em, H"ohere mathematik f"ur ingenieure bandiiigew"ohnliche differentialgleichungen, distributionen, integtraltransformationen, 3. ed., Teubner Verlag, Stuttgart, 1993.
BHW94
to3em, H"ohere mathematik f"ur ingenieure bandivvektoranalysis und funktionentheorie, 2. ed., Teubner Verlag, Stuttgart, 1994.
Bin97
K. Binder, Applications of monte carlo methods forstatisticalphysics, Rep. Prog. Phys. 60 (1997), 487-559.
BK97a
O.M. Becker and M. Karplus, JCP 106 (1997), 1495.
BK97b
Kurt Binder and Walter Kob, How can computer simulations contribute tounderstandthe static structure of glasses ?, cond-mat/9712011 (1997).
BK97c
Arnaud Buhot and Werner Krauth, Numerical solution of hard-core mixtures, cond-mat/9712092 (1997).
BLD+01
B. Bothner, W. S. Lewis, E. L. DiGammarino, S. J. Bothner, and R. W. Kriwacki, J. Molec. Biol. 314 (2001), 263.
BM60
V. Bargmann and M. Moshinsky, Group theory of harmonic oscillators(i). thecollective modes, Nucl. Phys. 18 (1960), 697-712.
BM61
to3em, Group theory of harmonic oscillators(ti). theintegrals of motion for thequadrupole-quadrupoleinteraction, Nucl. Phys. 23 (1961), 177-199.
BMa95
Carles Bona, Joan Masso, and Edward Seidel andJoanStela, A new formalism for numerical relativity, Phys. Rev. Lett. 75 (1995), 600-603.
BN91
B. A. Berg and T. Neuhaus, Phys. Letters B267 (1991), 249.
BN92
to3em, 9.
Bor94
Peter Borrmann, Path integral density functional theory, cond-mat/9412117 (1994).
BOW01
C. L. Brooks, J. N. Onuchic, and D. J. Wales, Taking a walk on a landscape, Science 293 (2001), 612.
BOWG92
David N. Beratan, José Nelson Onuchic, JayR. Winkler, and HarryB. Gray, Electron-tunneling pathways in proteins, Science 258 (1992), 1740-1741.
BPD97
Jacob Barhen, Vladimir Protoposecu, and DavidReister, Trust : A deterministic algorithm for globaloptimization, Science 276 (1997), 1094-1097.
BPE+97
Dik Bouwmeester, Jian-Wei Pan, Klaus Mattleand Manfred Eibl, Harald Weinfurter, and AntonZeilinger, Experimental quantum teleportation, Nature 390 (1997), 575.
BPR97
Jacob Barhen, Vladimir Protoposecu, and David Reister, Trust : A deterministic algorithm for global optimization, Science 276 (1997), 1094-1097.
BPTW81
T.L. Blundell, J.E. Pitts, I. J. Tickle, and S.P. Woodand C.-W. Wu, X-ray analysis of avian pancreatic polypeptide, Proc. Natl. Acad. Sciences (USA) 7 (1981), 4175, 1PPT.
BR66
Rudolf G. Buser and Dietolf Ramm, Laser pumping by intense discharges in$-pinchgeometry, App. Opt. 5 (1966), no. 4, 627-631.
BR96
Armin Bunde and H. Eduardo Roman, Gesetzmäsigkeiten der unordnung, Physik in unserer Zeit 6 (1996), 246-256.
Bru97
Pierpaolo Bruscolini, A coarse-grained, ``realistic'' model forproteinfolding, cond-mat/9707259 (1997).
BS87
Arno Br"uning and Karlheinz Spallek, Zahl und zuordnung 9, Schroedel Schulbuchverlag, 1987.
BS88
to3em, Zahl und zuordnung 10, Schroedel Schulbuchverlag, 1988.
BS+91a
I.N. Bronstein, K.A. Semendjajew, et al., Erg"anzende kapitel zu taschenbuch der mathematik, 6. ed., Verlag Harri Deutsch, Frankfurt a.M., 1991.
BS+91b
to3em, Taschenbuch der mathematik, 25. ed., Teubner Verlag, Stuttgart, 1991.
BS98
Kamal K. Bhattacharya and James P. Sethna, Multicanonical methods vs. molecular dynamicsvs.monte carlo : Comparison for lennard-jonesglasses, Phys. Rev. E 57 (1998), 2553.
BS01
D. Baker and A. Sali, Protein structure prediction and structural genomics, Science 294 (2001), 93.
BSM97
L. Bellomonte and R.M. Sperandeo-Mineo, A statistical approach to the second lawofthermodynamics using a computer simulation, Eur. J. Phys. 18 (1997), 321-326.
BTR+01
R. Bonneau, J. Tsui, I. Ruczinski, D. Chivian, C. M. E. Strauss, and D. Baker, Rosetta in casp4: progress in ab-initio protein structure prediction, Proteins 45 (2001), 119-126.
Buc92
V. Buch, Treatment of rigid bodies by diffusion monte carlo:application to the para-h \cdots$h$oandortho-h \cdots$h$o clusters, J. Chem. Phys. 97 (1992), no. 1, 726-728.
BW89
Joseph D. Bryngelson and Peter G. Wolynes, Intermediates and barrier crossing in a randomenergymodel (with applications to protein folding, J. Chem. Phys. 93 (1989), 6902-6915.
BWF+00
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig andI.N. Shindyalov, and P.E. Bourne, The protein data bank, Nucleic Acids Research 28 (2000), 235, http://www.rcsb.org/pdb.
BY86
K. Binder and A.P. Young, Spin glasses : Experimental facts, theoreticalconcepts, and open questions, Rev. Mod. Phys. 58 (1986), no. 4, 801-976.
CA96
Costas D. Maranasand Christodoulos A. Floudas C.S. Adjiman, I.P. Androulakis, A global optimzation method, $\alpha$bb, for processdesign, Computers and Chemical Engineering 20 (1996), S419-424.
Car74
Henri Cartan, Differentialformen, BI-Wissenschaftsverlag, Mannheim;Wien;Z"urich, 1974.
CBaV+98
J.N. Champness, M.S. Bennett, F. Wien andR. Visse, W.C. Summers, P. Herdewijn andE. de Clerq, T. Ostrowski, and R.L. Jarvestand M.R. Sanderson, Exploring the active site of herpes simplexvirus type-1 thymidine kinase by x-ray crystallographyof complexes aciclovir and other ligands, Proteins 32 (1998), 350.
CBB93a
B.C. Cetin, J. Barhen, and J.W. Burdick, Terminal repeller unconstrained subenergy tunneling(trust) for fast global optimization, J. Optim. Theory Appl. 77 (1993), no. 1, 97-126.
CBB93b
to3em, Terminal repeller unconstrained subenergytunneling(trust) for fast global optimization, J. Optim. Theory Appl. 77 (1993), no. 1, 97-126.
CBRL01
H. Claußen, C. Buning, M. Rarey, and T. Lengbauer, Flexe: Efficient molecular docking consiudering protein structure variations, JMB (2001).
CC93
GyorgyG. Ferenczy andHarold A. Scheraga Christophe Chipot, János G. Ángyán, Transferable net atomic charges from a distributedmultipole analysis forthe description ofelectrostatic properties. a case study ofsaturatedhydrocarbnos, J. Phys. Chem. 97 (1993), no. 25, 6628-6636.
CCW99
P.S. Charifson, J.J. Corkery, and M.A. Murckoand W.P. Walters, Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensionalstructures into proteins, J. Med. Chem. 42 (1999), 5100.
CD96
Hue Sun Chan and Ken A. Dill, Comparing folding codes for proteins and polymers, PROTEINS: Structure, Function, and Genetics 24 (1996), 335-344.
CF90
Cyrus Chothia and Alexei V. Finkelstein, The classification and origins of proteinfoldingpatterns, Annu. Rev. Biochem. 59 (1990), 1007-1039.
CH98
D. Cule and T. Hwa, Polymer reptation in disordered media, Phys. Rev. Lett. 80 (1998), 3145.
Cha43
S. Chandrasekhar, Stochastic problems in physics and astronomy, Rev. Mod. Phys. 15 (1943), 1.
Che97
Kan Chen, A general learning algorithm for solvingoptimizationproblems ans its application to the spinglass problem, adap-org/9704004 (1997).
Cho92
Cyrus Chothia, One thousan families for the molecular biologist, Nature 357 (1992), 543-544.
Cla97
Charles W. Clark, Closed-form solutions of the schrödingerequationfor a class of smoothed coulomb potentials, physics/9704019 (1997).
CLS95a
J. Cislo, L. Lopuszanski, and P.C. Stichel, On certain class of langrange functions with common equations of motion but various poissonbrackets, Fortschr. Phys. 43 (1995), no. 8, 745-762.
CLS95b
to3em, On langrange functions yielding the samerotationallycovariant euler variation, Fortschr. Phys. 43 (1995), no. 8, 733-744.
CMS92
Christophe Chipot, Bernard Maigret, and Jean-LouisRivailand Harold A. Scheraga, Modeling amino acid side chains. 1. determination ofnet atomic chargesfrom ab initioself-consistent-field molecular electrostaticproperties, J. Phys. Chem. 96 (1992), 10276-10284.
CNR73
C.J. Chen, N.M. Nerheim, and G.R. Russell, Double-discharge copper vapor laser withcopperchloride as a lasant, Appl. Phys. Lett. 23 (1973), no. 9, 514-515.
Cri96
G. M. Crippen, J. Molec. Biol. 260 (1996), 467-475.
CSW94
Thomas Coleman, David Shalloway, and Zhijun Wu, A parallel build-up algorithm for globalenergyminimzations of molecular clusters usingeffectiveenergy simulated annealing, J. Glob. Opt. 4 (1994), 171-185.
dAC94
J.R.L. de Almeida and S. Coutinho, Spin glass : an unfinished story, cond-mat/9411053 (1994).
Dav75
Ernest R. Davidson, The iterative calculation of a few of tehlowesteigenvalues and corresponding eigenvectors oflargereal-symmetric matrices, J. Comp. Phys. 17 (1975), 87-94.
Dav99
A. P. Davis, Synthetic molecular motors, Nature 401 (1999), 120-121.
dCP62
Jacques des Cloizeaux and J.J. Pearson, Spin-wave spectrum of the antiferromagneticlinearchain, Phys. Rev. 128 (1962), no. 5, 2131-2135.
Der97
Philippe Derreumaux, A diffusion process-controlled monte carlo methodforfinding the global energy minimum of apolypeptidechain. i. formulation and test on ahexadecapeptide, J. Chem. Phys. 106 (1997), no. 12, 5260-5270.
Deu91
Peter Deuflhard, Numerische mathematik, de Gruyter, Berlin, New York, 1991.
DeV96
Paul L. DeVries, Resource letter cp-1: Computational physics, Am. J. Phys. 64 (1996), no. 4, 364-368.
DFW+01
E. L. DiGammarino, I. Filippov, J. D. Weber, B. Bothner, and R. W. Kriwacki, Biochemistry 40 (2001), 2379.
DHL98
Dirk Drasdo, T. Hwa, and Michael L"assig, Scaling laws and similarity detection insequencealignment with gaps, J. Comp. Biol. (1998).
Dit96a
Frank-Michael Dittes, Optimization on rugged landscapes: A new general purpose monte carloapproach, Phys. Rev. Lett. 76 (1996), no. 25, 4651-4655.
Dit96b
to3em, Optimization on rugged landscapes: A newgeneralpurpose monte carlo approach, Phys. Rev. Lett. 76 (1996), no. 25, 4651-4655.
DJS+98
X. Daura, B. Juan, D. Seebach, W.F. van Gunsteren, A. E. MarX. Daura, B. Juan, D. Seebach, W.F. van Gunsteren, and A. E. Mark, J. Molec. Biol. (1998), 925.
DK98
Y. Duan and P. A. Kollman, Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution, Science 23 (1998), 740.
Dob01
C. M. Dobson, Biochem. Soc. Symp. (2001), 1-26.
DSS+01
A. R Dinner, A. Sali, L. J. Smith, C. M. Dobson, and M. Karplus, Understanding protein folding via free energy surfaces from theory and experiment, Trends in Structural Biology 25 (2001), 331.
DV99
David D. Diller and Christophe L.M.J. Verlinde, A critical evaluation of several global optimization algorithms for the purpose of molecular docking, J. Comp. Chem. 20 (1999), 1740.
DW96
J. P.K. Doyle and D. Wales, 8428.
DW97
Jonathan P.K. Doye and David J. Wales, On the thermodynamics of global optimization, cond-mat/9709019 (1997).
DW98a
J. P.K. Doye and D. Wales, 1357.
DW98b
to3em, 1357.
DW98c
to3em, 1357.
ea57
C.S. Wu et al., Experimental test of parity conservation in betadecay, Phys. Rev. 105 (1957), 1413-1415.
EA75
S.F. Edwards and P.W. Anderson, Theory of spin glasses, J. Phys. F.:Metal Phys. 5 (1975), 965-974.
ea88
M. E. Newcomer et. al., JEMBO J. 7 (1988), 1597.
ea94
M.D. Cable et al., Indirectly driven, high conergenceinertialconfinement fusion implosions, Phys. Rev. Lett. 73 (1994), no. 17, 2316-2319.
ea95
William H. Press et al, Numerical recipies in c, Cambridge University Press, Cambridge, 1995.
EH97
Frank Eisenmenger and Ulrich H.E. Hansmann, Variation of the energy landscape of a smallpeptideunder a change from the ecepp/2 force fieldto ecepp/3, physics/9710020 (1997).
EM86
D. Eisenberg and A. D. McLachlan, Solvation energy in protein folding and binding, Nature 319 (1986), 199-203.
EN93a
A. Enders and G. Nimtz, Evanescent-mode propagation and quantum tunneling, Phys. Rev. E 48 (1993), no. 1, 632-634.
EN93b
to3em, Photonic-tunneling experiments, Phys. Rev. B 47 (1993), no. 15, 9605-9609.
End99
S. A: Endow, Determinants of molecular motor directionality, Nature Cell Biology 1 (1999), E163-E167.
Erm98
Bard Ermentrout, Neural networks as spatio-temporalpattern-formingsystems, Rep. Prog. Phys. 61 (1998), 353-430.
ES70
E. Engelhard and F. Spieweck, Ein ionen-laser für metrologische anwendungen, Z.Naturforsch. 25a (1970), 156.
Fah74
Theodore S. Fahlen, Hollow-cathode copper-vapor laser, J. App. Phys. 45 (1974), no. 9, 4132-4133.
FBPN97
Helge Frauenkorn, Uga Bastolla, Erwin Gerstnerand PeterGrassberger, and Walter Nadler, A new monte carlo algorithm for protein folding, cond-mat/9705146 (1997).
Fei78
Mitchell J. Feigenbaum, Quantitative universality for a class ofnonlineartransformations, J. Stat. Phys. 19 (1978), no. 1, 25-52.
Fer99
A. Fersht, Structure and mechanism in protein science, Freeman, New York, 1999.
Fie98
Martyn R. Field, Optimizing a parallel conjugate gradient solver, SIAM J. Sci. Comput. 19 (1998), no. 1, 27-37.
Fis86
Gerd Fischer, Lineare algebra, 9. ed., Vieweg Verlagsgesellschaft, Braunschweig, 1986.
FK96
Satoshi Fujimoto and Norio Kawakami, Competition between the mott transition andtheanderson localisation in 1d disorderedinteractingelectron systems, cond-mat/9609011 (1996).
FP83
J.L. Fauchere and V. Pliska, Eur. J. med. Chem.-Chim. ther. 18 (1983), 369-375.
Gab97
M. Gabb, JMB 272 (1997), 106.
GAH96
S. K. Gregurick, M. H. Alexander, and B. Hartke, JPC 104 (1996), 2684.
GAS96
A.M. Gutin, V.I. Abkevich, and E.I. Shakhnovich, Chain length scaling of protein folding time, Phys. Rev. Lett. 77 (1996), no. 27, 5433-5436.
GC94
Jonathon K. Gregory and David C. Clary, A comparison of conventional and rigid bodydiffusionmonte carlo techniques. application towater dimer, Chem. Phys. Lett. 228 (1994), 547-554.
GCLY76
E. Clementi George C. Lie and M . Yoshimine, Study of the structure of molecularcomplexes. xiii.monte carlo simulation of liquidwater with aconfiguration interaction pairpotential, J. Chem. Phys. 64 (1976), no. 6, 2314-2323.
GCZ97
M. Marsili G. Caldarelli and Y.-C. Zhang, A prototype model of stock exchange, cond-mat/9709118 (1997).
Ge90
Renpu Ge, A filled function method for finding aglobalminimizer of a function of several variables, Mathematical Programming 46 (1990), 191-204.
GFEG97
S. K. Gregurick, E. Fredj, R. Elber, and R. B. Gerber, JPC 101 (1997), 8595.
GG96
George Gloeckler and Johannes Geiss, Abundance of $^3$he in the local interstellar cloud, Nature 381 (1996), 210-211.
GJG95
P. Willett G. Jones and R. C. Glen, JMB 245 (1995), 43.
GLBG03
S. K. Gregurick, J. H.-Y. Liu, D. A. Brant, and R. B. Gerber, JPC 3476 (103), 1999.
GM74
Philip E. Gill and Walter Murray, Newton-type methods for unconstrained andlinearlyconstrained optimization, Math. Prog. 7 (1974), 311-350.
GO90
D.S. Goodsell and A.J. Olson, Automated docking of substrates to proteins by simulatedannealing, Proteins 8 (1990), 195.
Gol82
M. J. E. Golay, IEEE Trans. Inform. Theory 28 (1982), 543.
Gol89
David E. Goldberg, Genetic algorithms in search, optimization, andmachine learning, Addison-Wesley, Reading, Massachusetts, 1989.
GS69
N. Go and H. A. Scheraga, Analysis of the contribution of internal vibrations to the statistical weight of equilibirium conformations of macromolecules, J. Chem. Phys. (1969).
GS76
to3em, On the use of classical statistical mechanics in the treatment of polymer chain conformation, Macromolecules 9 (1976), 535-542.
GS90
Kenneth D. Gibson and Harold A. Scheraga, Dynamics of peptides with fixed geometry :kineticenergy terms and potential energy derivativesasfunctions of dihedral angles, J. Comp. Chem. 11 (1990), no. 4, 487-492.
GS94
to3em, A rapid and efficient algorithm forpackingpolypeptide chains by energy minimizations, J. Comp. Chem. 15 (1994), no. 12, 1403-1413.
GT77
S. Grossmann and S. Thomae, Invariant distributions and stationarycorrelationfunctions of one-dimensional discreteprocesses, Z. Naturforsch. 32 a (1977), 1353-1363.
GVaS+95
D.K. Gehlhaar, G.M. Verkhivker, P.A. Rejto andC.J. Sherman, D.B. Fogel, L.J. Fogel, and S.T. Freer, Molecular recognition of the inhibitor ag-1343 by hiv-1protease: conformationally flexible docking by evolutionaryprogramming, Chem. Biol. 2 (1995), 317.
Ha97
Ulrich H.E. Hansmann and Masato Masuya and Yuko Okamoto, Characteristic temperatures of folding of asmallpeptide, Proc. Natl. Acad. Sci. USA 94 (1997), 10652-10656.
Hab88
Klaus Habetha, H"ohere mathematik f"ur ingenieure und physikerbandiii, Ernst Klett Verlag, Stuttgart, 1988.
Hab90
to3em, H"ohere mathematik f"ur ingenieure und physiker bandi, Ernst Klett Verlag, Stuttgart, 1990.
Hab91
to3em, H"ohere mathematik f"ur ingenieure und physikerbandii, Ernst Klett Verlag, Stuttgart, 1991.
Han99a
U. H. E. Hansmann, Eur. Phys. J. B 12 (1999), 607.
Han99b
Eur. Phys. J. B 12 (1999), 607.
Han02
H.U.E. Hansmann, Global optimization by energy landscpae paving, Phys. Rev. Letters 88 (2002), 068105.
Har62
Thomas E. Hartman, Tunneling of a wave packet, J. Appl. Phys. 33 (1962), no. 12, 3427-3429.
HB94
Klaus Hass and Paul Busch, Causality of superluminal barrier traversal, Phys. Lett. A 185 (1994), 9-13.
HC73
H. Kistenmacher H.Popkie and E. Clementi, Study of the structure of molecularcomplexes. iv. thehartree-fock potential for thewater dimer and itsapplication to the liquid state, J. Chem. Phys. 59 (1973), no. 3, 1325-1336.
HCX99
T.J.W. Hou, L. Chen, and X. Xu, Automated docking of peptides and proteins by using a geneticalgorithm combined with a tabu search, Protein Eng. 12 (1999), 639.
Heb87
Gerhard Heber, Mathematische hilfsmittel der physik, 2. ed., Verlag Zimmermann-Neufang, Ulmen, 1987.
Heu90
Hans-Otto Heuer, A fast vectorized fortran 77 program for themontecarlo simulation of the three-dimensional isingsystem, Computer Physics Communication 59 (1990), 387-398.
HHS88
W. Hasel, T. F. Hendrickson, and W. C. Still, Thethraedon Comput. Methodol. 1 (1988), 103.
HJS50
Otto Haxel, J.H.D. Jensen, and Hans E. Suess, Modellmäsige deutung derausgezeichnetennukleonenzahlen im kernbau, Zeitschrift für Physik 128 (1950), 295-311.
HL98
Terence Hwa and Michael L"assig, Optimal detection of sequence similarity bylocalalignment.
HLW96a
Chao Tang Hao Li, Robert Helling and NedS. Wingreen, Emergence of preffered structures in a simple modelofprotein folding, Science 273 (1996), 666-669.
HLW96b
to3em, Why do proteins look like proteins, cond-mat/9603016 (1996).
HLW97
Chao Tang Hao Li and Ned S. Wingreen, Are protein folds atypical ?, cond-mat/9709083 (1997).
HMO97
Ulrich H.E. Hansmann, Masato Masuya, and Yuko Okamoto, Characteristic temperatures of folding of a small peptide, Proc. Natl. Acad. Sci. USA 94 (1997), 10652-10656.
HMW02
T. Herges, H. Merlitz, and W. Wenzel, Stochastic optimisation methods for biomolecular structure prediction, J. Ass. Lab. Autom. 7 (2002), 98-104.
HMY97
Ulrich H.E. Hansmann, Masato Masuya, and YukoOkamoto, Characteristic temperatures of folding of a smallpeptide, Proc. Natl. Acad. Sci. USA 94 (1997), 10652-10656.
HN94
W. Heitmann and G. Nimtz, On causality proofs of superluminal barriertraversalof frequency band limited wave packets, Phys. Lett. A 196 (1994), 154-158.
HN96
Koji Hukushima and Koji Nemoto, Exchange monte carlo method and application tospinglass simulations, Journal of the Physical Society of Japan 65 (1996), no. 6, 1604-1608.
HO97
Ulrich H.E. Hansmann and Yuko Okamoto, Numerical comparison of three recentlyproposedalgorithms in the protein folding problem, J. Comput. Chem 18 (1997), 920.
HO99
U.E. Hansmann and Y. Okamoto, JPC B 103 (1999), 1595.
HOF96a
Ulrich H.E. Hansmann, Yuko Okamoto, and FrankEisenmenger, Molecular dynamics, langevin and hybrid monte carlosimulations in a multicanonical ensemble, Chem. Phys. Lett. 259 (1996), 321-330.
Hof96b
Holger F. Hofmann, A dynamical model of the chemical bond: kineticenergyresonances between atomic orbitals, physics/9612007 (1996).
Hof97
Gary G. Hoffman, An integral for second-order multiplescatteringperturbation theory, J. Comp. Phys. 130 (1997), 129-135.
Hol92
John H. Holland, Genetische algorithmen, Spektrum der Wissenschaft (1992), no. 9, 44-51.
Hon99
B. Honig, Protein folding: From the levinthal paradox to structure prediction, JMB 293 (1999), 283.
HS74
B. Hesselbo and R. B. Stinchcombe, 1995.
HSBW03
T. Herges, A. Schug, B. Burghardt, and W. Wenzel, Low energy conformations of a three helix peptide in an all-atom biomolecular forcefield, Intl. J. Quantum Chem. (2003), (in press).
HW98
Stura E.A. Yli-Kauhaluoma J.T. Gao C. Deng-Q. Beno B.R. Houk K.N. Janda K.D. Heine, A. and I.A. Wilson, Science 279 (1998), 1934.
HW99
K. Hamacher and W. Wenzel, Phys. Rev.iew E 59 (1999), 938.
HW03
T. Herges and W. Wenzel, Reproducible in-silico folding of a three-helix protein in a transferable all-atom forcefield, Angew. Chemie. Intl. Ed. (2003), (submitted).
IA95
Costas D. Maranas andChristodoulos A. Floudas I.P. Androulakis, $\alpha$bb: A global optimization method for generalconstrained nonconvex problems, J. Glo. Opt. 7 (1995), 1-27.
Ibe95
Hans Karl Iben, Tensorrechnung, B.G. Teubner Verlagsgesellschaft, Stuttgart, 1995.
IGA84
Yin Sing Ching Ian Galbraith and Eitan Abraham, Two-dimensional time-dependentquantum-mechanicalscattering event, Am. J. Phys. 52 (1984), no. 1, 60-68.
INaZaS97
Toshiaki Iitaka, Shintaro Nomura, HidekiHirayama andXinwei Zhao, and Yoshinobu Aoyagi andTakuo Sugano, Calculating teh linear response functions ofnon-interactingelectrons by the time-dependentschrödinger equation, cond-mat/9703224 (1997).
IPaS96
Anders Irbäck, Carsten Peterson, and FrankPotthast andOla Sommelius, Local interactions and protein folding : A 3doff-lattice approach, cond-mat/9610010 (1996).
IPaS97
Anders Irbäck, Carsten Peterson, and FrankPotthast andErik Sandelin, A novel monte carlo procedure for protein design, cond-mat/9711092 (1997).
Jan52
L. Janossy, The passage of a wave packet through apotentialbarrier, Acta. Phys. Acad. Hung. Sci. 2 (1952), 172-174.
JBH98
C.W. Johnson, G.F. Bertsch, and W.D. Hazelton, A lanczos algorithm for linear response, physics/9802014 (1998).
JHW63
Jr. Joe H. Ward, Hierarchical grouping to optimize anobjectivefunction, Journal of the American Statistical Association 58 (1963), 236-244.
JM97
W.L. Jorgensen and N.A. McDonald, Development of an all-atom force field for heterocycles.properties of liquid pyridine and diazenes, J. Mol. Struct. 424 (1997), 145.
JM98
W. L. Jorgensen and N. A. McDonald, Development of an all-atom force field for heterocycles, J. Mol. Struct. 424 (1998), 145.
JWGT97
G. Jones, P. Wilett, R.C. Glen, and A.R. Leachand R. Taylor, Development and validation of a genetic algorithmfor flexible docking, J. Mol. Biol. 267 (1997), 721.
Kab96
Winfried Kaballo, Einf"uhrung in die analysis i, Spektrum Akademischer Verlag, Heidelberg, 1996.
KBOF82
I.D. Kuntz, J.M. Blaney, S.J. Oatley, and R. Langridgeand T.E. Ferrin, A geometric approach to macromolecule-ligand interactions, J. Mol. Biol. 161 (1982), 269.
KC97
Mehul M. Khimasia and Peter V. Coveney, Protein structure prediction as a hardoptimizationproblem : the gentic algorithm approach, cond-mat/9708012 (1997).
KES97
C. Keasar, R. Elber, and J. Skolnick, Folding and Design 1 (1997), 247.
KFS97
Ioan Kosztin, Byron Faber, and Klaus Schulten, Introduction to the diffusion monte carlo method, cond-mat/9702023 (1997).
KGV83
S. Kirkpatrick, C.D. Gelatt, and M.P. Vecchi, Optimization by simulated annealing, Science 220 (1983), 671-680.
KK97
Toshikatsu Koga and Katsutoshi Kanayma, Noninteger principal quantum numbers increasetheefficiency of slater-type basis sets : singlychargedcations and anions, J. Phys. B : At. Mol. Opt. Phys. 30 (1997), 1623-1631.
KKC86
G.C. Lie K.S. Kim, M. Dupuis and E. Clementi, Revisiting small clusters of water molecules, Chem. Phys. Lett. 131 (1986), no. 6, 451-456.
Kli95
Djurdje Cvijovicand Jacek Klinowski, Taboo search : An approach to the multipleminimaproblem, Science 267 (1995), 664-666.
KLK99
E. H. Koo, P. T. Landsbury, and J. W. Kelly, Proc. Natl. Acad. <Sci.(USA) 96 (1999), 9989.
KM66
P. Kramer and M. Moshinsky, Group theory of harmonic oscillators(iii). stateswith permutational symmetry, Nucl. Phys. 82 (1966), 241-274.
KM95
W. Krauth and M. Mezard, Z. Phys. B 97 (1995), 127.
Kob80
J.A. Kobussen, On a systematic search for integrals of the motion, Helvetica Physica Acta 53 (1980), 183-200.
KP90
Martin Karplus and Grefory A. Petsko, Molecular dynamics simulations in biology, Nature 347 (1990), 631-639.
KP91
Jaroslaw Kostrowicki and Lucja Piela, Diffusion equation method of global minimization:performance for standard test functions, J. Optim. Theory Appl. 69 (1991), no. 2, 269-284.
KPCS91
J. Kostrowicki, L. Piela, B.J. Cherayil, and H.A. Scheraga, Performance of the diffusion equation method insearches for optimumstructures of clusters oflennard-jones atoms, J. Phys. Chem. 95 (1991), 4113-4119.
KS95
Jaroslaw Kostrowicki and Harold A. Scheraga, Simple global minimization algorithm forone-variablerational functions, J. Glo. Optim. 6 (1995), 293-311.
KT97
D.K. Klimov and D. Thirumalai, Viscosity dependence of the folding rates ofproteins, cond-mat/9705309 (1997).
Kub66
R. Kubo, The fluctuation-dissipation theorem, Rep. Prog. Phys. 29 (1966), 255-284.
Kv95
Martin Karplus and Andrej Šali, Theoretical studies of protein folding andunfolding, Current Opinion in Structural Biology 5 (1995), 58-73.
KV96
Dimitris J. Kavvadias and Michael N. Vrahatis, Locating and computing all the simple rootsandextrema of a function, SIAM J. Sci. Comput. 17 (1996), no. 5, 1232-1248.
L+89
Wilhelm Leupold et al., Lehr- und "ubungsbuch mathematik band iii, VEB Fachbuchverlag, Thun, 1989.
LAC+02
A. Liwo, P. Arlukowicz, C. Czaplewski, S. Oldizeij, J. Pillardy, and H.A. Scheraga, A method for optimising potential energy functions by a hierarchichal design of the potential energy landscape, Proc. Natl. Acad. <Sci.(USA) 99 (2002), 1937-1942.
Lan86
Christopher G. Langton, Studying artifical life with cellular automata, Physica D 22 (1986), 120-149.
Lat01
E.E. Lattman, Casp4, Proteins 44 (2001), 399.
LaVSVV92
A. P. Lyubartsev, A.A. Martinovski andS. V. Shevkunov, and P.N. Vorontsov-Velyaminov, JCP 96 (1992), 1776.
LB89
J.H. Holland L.B. Booker, D.E. Goldberg, Classifier systems and genetic algorithms, Artificial Intelligence 40 (1989), 235-282.
LC76
Michael Levitt and Cyrus Chothia, Structural patterns in globular proteins, Nature 261 (1976), 552-558.
LD89
K.F. Lan and K.A. Dill, Macromolecules 22 (1989), 3986.
LDSH03
L. L. Looger, M. A. Dwyer, J. J. Smith, and H. W. Hellinga, Computational design of receptor and sensor proteins with novel functions, Nature 423 (2003), 185-190.
Lee93a
J. Lee, 211.
Lee93b
to3em, 211.
Lee93c
to3em, 211.
Lev68
Cyrus Levinthal, Are there pathways for protein folding ?, J. Chim. Phys. 65 (1968), 44-45.
Lev95
Barbara Goss Levi, Researchers report evidence for lasingwithoutinversion, Physics Today (1995), 19-20.
LK66
I.M. Lifshitz and A.M. Kosevich, The dynamics of a crystal lattice with defects, Rep. Prog. Phys. 29 (1966), 217-254.
LK97
Themis Lazaridis and Martin Karplus, ``new view'' of protein folding reconciled withtheold through multiple unfolding simulations, Science 278 (1997), 1928-1931.
LK98
T. Lazaridis and M. Karplus, Dscrimination of the native from misfolded protein models with anenergy function includind implicit solvation., J. Molec. Biol. 288 (1998), 447.
LM85
A. V. Levy and A. Montalvo, The tunneling algorithm for the global minimizationoffunctions, SIAM J. Sci. Stat. Comput. 6 (1985), no. 1, 15-29.
LM94
R. Landauer and Th. Martin, Barrier interaction time in tunneling, Rev. Mod. Phys. 66 (1994), no. 1, 217-228.
Lor99
D. M. Lorber, Chemistry and Biology 6 (1999), R227, review.
LR71
B. K. Lee and F. M Richards, J. Molec. Biol. 79 (1971), 351.
LS87
Z. Li and H.A. Scheraga, Proc. Nat. Acad. Sci. U.S.A. 84 (1987), 6611.
LS89a
Millard J. Lambert and Harold A. Scheraga, Pattern recognition in the prediction ofproteinstructure. i. tripeptide conformationalprobabilitiescalculated from the amino acidsequence, J. Comp. Chem. 10 (1989), no. 6, 770-797.
LS89b
to3em, Pattern recognition in the prediction ofproteinstructure. ii. chain conformation fromaprobability-directed search procedure, J. Comp. Chem. 10 (1989), no. 6, 798-816.
LS89c
to3em, Pattern recognition in the prediction ofproteinstructure. iii. an importance-samplingminimizationprocedure, J. Comp. Chem. 10 (1989), no. 6, 817-831.
LSB+02
H. Liu, J. J. Schmidt, G. D. Bachand, Shahir S. Rizkand L. L. Looger, H. W. Hellinga, and C. D. Montemagno, Control of a biomolecular motor-powered nanodevice with an engineered chemical switch, Nature Materials 1 (2002), 173-177.
LW99
M. Liu and S. Wang, Mcdock: a monte carlo simulation approach to the molecular docking problem, J. Comput.-Aided Mol. Des. 13 (1999), 435.
Man90
Karl Manteuffel, Spieltheorie, 3. ed., B.G. Teubner Verlagsgesellschaft, Leipzig, 1990.
Man95
V.I. Man'ko, Introduction to quantum optics, quant-ph/9509018 (1995).
Man97
Riccardo Mannella, Numerical integration of stochasticdifferentialequations, cond-mat/9709326 (1997).
MaNRTT53
N. Metropolis, A. W. Rosenbluth andM. N. Rosenbluth, A. H. Teller, and E. Teller, Equation of state calculations by fast computingmachines, J. Chem. Phys. 21 (1953), no. 6, 1087-1092.
MB97
C. McMartin and R. Bohacek, Qxp: Powerful, rapid computer algorithms for structure-baseddrug design, J. Comput.-Aided Mol. Des. 11 (1997), 333.
MBAS97
Christian Micheletti, Jayanth R. Banavar, AmosMaritan, and Flavio Seno, Steric constraints in model proteins, cond-mat/9712277 (1997).
MBW03
H. Merlitz, B. Burghardt, and W. Wenzel, Application of the stochastic tunneling method to high throughput screening, Chem. Phys. Lett. 370 (2003), 68.
MDW99
M. A. Miller, J. P.K. Doye, and D. Wales, 328.
Mey96
David A. Meyer, Quantum mechanics of lattice gas automata -i. oneparticle plane waves and potentials, quant-ph/9611005 (1996).
MF94
Costas D. Maranas and Christodoulos A. Floudas, Global minimum energy potential conformations ofsmallmolecules, J. Glo. Opt. 4 (1994), 135-170.
MF97
to3em, A global optimzation approach forlennard-jonesmicroclusters, J. Chem. Phys. 97 (1997), no. 15, 7667-7678.
MFZH01
J. Moult, K. Fidelis, A. Zemia, and T. Hubbard, Critical assessment of methods of protein structure (casp): round iv, Proteins 45 (2001), 2-7.
MG76
S. Miyashiro and H. Grönig, Messung an einem n$-lasermitdämpfungskondensatoren, Z.Naturforsch. 31a (1976), 1433-1434.
MGJ+03
U. Mayor, N. R. Guydosh, C. M. Johnson, J. G. Grossmann, S. Sato, G. S. Jas, S. M. V. Freund, D. O. V. Alonso, V. Daggett, and A. R. Fersht, The complete folding pathway of a protein from nanoseconds to micorseconds, Nature 421 (2003), 863-867.
MJB+98
A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus, All-atom empirical potential for molecular modeling and dynamics studies of proteins, J. Phys. Chem. B102 (1998), 3586.
ML92
Th. Martin and R. Landauer, Time delay of evanescent electromagnetic waves andtheanalogy to particle tunneling, Phys. Rev. A 45 (1992), no. 4, 2611-2617.
MMaAS75
F.A. Momany, R.F. McGuire, and A.W. Burgess andHarold A. Scheraga, Energy parameters in polypeptides. vii. geometricparameters, partial atomic charges, nonbondedinteractions, hydrogen bond interactions, andintrinsic torsional potentials for thenaturallyoccuring amino acids, J. Phys. Chem. 79 (1975), no. 22, 2361-2381.
Mor98
G. M. Morris, Automated dockingusing a lamarckian genetic algorithm and an empirical bindingfree energy function, J. Comp. Chem. 19 (1998), 1639.
MP19
E. Marinari and G. Parisi, 1992.
MP92
to3em, Simulated tempering: A new monte carlo scheme, Europhys. Lett. 19 (1992), 451.
MQ71
M. Moshinsky and C. Quesne, Linear canonical transformations and theirunitaryrepresentations, J. Math. Phys. 12 (1971), no. 8, 1772-1783.
MS01
G. Woehlke M. Schliewa, Molecular motors: Switching on kinesin, Nature 411 (2001), 424-425.
MSAB97
Christian Micheletti, Flavio Seno, AmosMaritan, and Jayanth R. Banavar, Inverse design of proteins with hydrophobic andpolar amino acids, cond-mat/9712124 (1997).
MW80
M. Moshinsky and P. Winternitz, Quadratic hamiltonians in phase space andtheireigenstates, J. Math. Phys. 21 (1980), no. 7, 1667-1682.
MW90
Meinhold and Wagner, Partielle differentialgleichungen, 6. ed., B.G. Teubner Verlagsgesellschaft, Leipzig, 1990.
MW93
Gerhard Merziger and Thomas Wirth, Repetitorium der h"oheren mathematik, 2. ed., Binomi Verlag, Hannover, 1993.
MW02
H. Merlitz and W. Wenzel, Comparison of stochastic optimization methods forreceptor-ligand docking, Chem. Phys. Lett. 362 (2002), 271.
NCP+03
M. Nanias, M. Chinchio, J. Pillardy, D. R. Ripoll, and H. A. Scheraga, Packing helices in proteins by global optimization of a potential energy function, Proc. Natl. Acad. <Sci.(USA) 100 (2003), 1706-1710.
ND96
Jiang S. Strick K. L. Li Y.-Y. Neurath, A. R. and A. K. Debnath, Nature Medicine 2 (1996), 230.
Ner77
Noble M. Nerheim, A parametric study of the copper chloride laser, J. App. Phys. 48 (1977), no. 3, 1186-1190.
NFA02
J. W. Neidigh, R. M. Fesinmeyer, and N. H. Anderson, Nature Struct. Biol. 9 (2002), 425.
NGB+02
C. Niocolau, R. Geferath, T. S. Balaban, J.E.Lazarte, and R. J. Hopkins, A liposome-base therapuetic vaccine against beta-amylod plaques on the pancreas of transgenic norba mice, Proc. Natl. Acad. <Sci.(USA) 99 (2002), 2332.
NGH90
Kyoung Tai No, J. Andrew Grant, and HaroldA.Scheraga, Determination of net atomic charges using amodifiedpartial equalization of orbitalelectronegativitymethod. 1. application to neutralmolecules as modelsfor polypeptides, J. Phys. Chem. 94 (1990), 4732-4739.
NGN
Hugh Nymeyer, Angel E. Garcia, and José NelsonOnuchic, Folding funnels and frustration in off-latticeminimalist protein landscapes, Proc. Nat. Acad. Sci., (in press).
NGP+92
G. Nemethy, K. D. Gibson, K. A. Palmer, C. N. Yoon, G. Paternali, A. Zagari, S. Rumsey, and H.A. Scheraga, Energy parameters in polypeptides 10. improved geometrical paramters and nonbonded interactions for use in the ecepp/3 algorithm., J. Phys. Chem. 96 (1992), 6472-6484.
NGS90
Kyoung Tai No, J. Andrew Grant, and HaroldA. Scheraga, Determination of net atomic charges using a modifiedpartial equalizationof orbital electronegativitymethod. 1. application to neutral molecules asmodels for polypeptides, J. Phys. Chem. 94 (1990), 4732-4739.
NGS95
Kyoung Tai No, J. Andrew Grant, and Mu Shik Jhonand Harold A. Scheraga, Determination of net atomic charges using a modifiedpartial equalizationof orbital electronegativitymethod. iv. application to hypervalent sulfur- andphosphorus-containing molecules, J. Comp. Chem. 16 (1995), no. 8, 1011-1026.
NM92
J.Thomas Ngo and Joe Marks, Computational complexity of a problem inmolecularstructure prediction, Protein Engineering 5 (1992), no. 4, 313-321.
NNY97
Muriel Ney-Nifle and A. Peter Young, Chaos in two-dimensional ising spin glass, J. Phys. A : Math. Gen. 30 (1997), 5311-5317.
NP96
Michael K. Ng and Robert J. Plemmons, Lms-newton adaptive filtering usingfft-basedconjugate gradient iterations, Electronic Transactions on Numerical Analyis 4 (1996), 14-36.
NPS83
George Nemethy, Marcla S. Pottle, and HaroldA. Scheraga, Energy parameters in polypeptides. 9. updating ofgeometrical parameters, nonbonded interactions, andhydrogen bond interactions for the naturallyoccuringamino acids, J. Phys. Chem. 87 (1983), 1883-1887.
NSaGW97
James C. Nelson, Jeffrey G. Saven, and JeffreyS. Moore andPeter G. Wolynes, Solvophobically driven folding of nonbiologicaloligmers, Science 277 (1997), 1793-1796.
NVS91
Akbar Nayeem, Jorge Vila, and Harold A. Scheraga, A comparative study of the simulated-annealing and monte carlo-with-minimization approaches to the minimum-energy structures of polypeptides: [met]-enkephalin, J. Comp. Chem. 12 (1991), no. 5, 594-605.
OaGW97
José Nelson Onuchic and Zaida Luthey-Schulten andPeter G. Wolynes, Theory of protein folding: The energy landscapeperspective, Annu. Rev. Phys. Chem. 48 (1997), 545-600.
OLSW97
José Nelson Onuchic, Zaida Luthey-Schulten, and Peter G. Wolynes, Theory of protein folding: The energy landscape perspective, Annu. Rev. Phys. Chem. 48 (1997), 545-600.
OMY76
E. Clementi O. Matsuoka and M . Yoshimine, Ci study of the water dimer potential surface, J. Chem. Phys. 64 (1976), no. 4, 1352-1361.
OPS93
K.A. Olszewski, L. Piela, and Harold A. Scheraga, Mean field theory as a tool for intramolecular conformational optimization. 3. Teston melittin, J. Phys. Chem. 97 (1993), 267-270.
Pap94a
Christos H. Papadimitriou, Computational complexity, Addison-Wesley, Reading, Massachusetts, 1994.
Pap94b
to3em, Computational complexity, Addison-Wesley, Reading, Massachusetts, 1994.
PB89
Peter Plaschko and Klaus Brod, H"ohere mathematische methoden f"ur ingenieureundphysiker, Springer Verlag, Berlin, 1989.
PCL+01
J. Pillardy, C. Czaplewski, A. Liwo, J. Lee andD. R. Ripoll, R. Kamierkiewicz, Stanislaw Oldziej andW. J. Wedemeyer, K. D. Gibson, Y. A. Arnautova, J. Saunders, Y.-J. Ye, and Harold A. Scheraga, Recent improvements in prediction of protein structure by global optimization of a potential energy function, Proc. Natl. Acad. <Sci.(USA) 98 (2001), 2329.
Per91
PM Perspektive, Die welt der zahlen, Gruner und Jahr AG, Hamburg, 1991.
Pes73
Ernst Peschl, Differentialgeometrie, BI-Wissenschaftsverlag, Mannheim, 1973.
Pip75
J.A. Piper, A copper iodide laser excited by transversedischarge, Opt. Comm. 14 (1975), no. 3, 296-300.
PKS89
L. Piela, J. Kostrowicki, and Harold A. Scheraga, The multiple-minima problem in the conformationalanalysis of molecules.deformation of the potentialenergy hypersurface by the diffusionequation method, J. Phys. Chem. 93 (1989), 3339-3346.
PL96
B. Park and M. Levitt, Energy functions that discriminate x-ray and near-native folds from well-constructed decoys, J. Molec. Biol. 258 (1996), 367.
PM97
J. T. Pedersen and J. Moult, J. Molec. Biol. 269 (1997), 240.
PS87
L. Piela and H.A. Scheraga, On the multiple-minima problem in theconformationalanalysis of polypeptides i. backbonedefrees of freedomfor a perturbed $\alpha$-helix, Biopolymers 26 (1987), S33-S58.
PS91
Kathleen A. Palmer and Harold A. Scheraga, Standard-geometry chains fitted to x-rayderivedstructures : Validation of therigid-geometryapproximation. i. chain closurethrough a limitedsearch of ``loop'' conformations, J. Comp. Chem. 12 (1991), no. 4, 505-526.
PS93
Stephan D. Pickett and Michael J.E. Sternberg, Empirical scale of side-chain conformational entropy in protein folding, JMB 231 (1993), 825-839.
PS97
PatrikÖhberg and Stig Steholm, A hartree-fock study of a bose condensed gas, J. Phys. B : At. Mol. Opt. Phys. 30 (1997), 2749-2760.
PSG94
Panos M. Pardalos, David Shalloway, and GuoliangXue, Optimization methods for computing global minimaofnonvoncex potential energy functions, J. Glob. Opt. 4 (1994), 117-133.
PTW98
J.J. Portman, S. Takada, and Peter G. Wolynes, Variational theory for site resolved proteinfoldingfree energy surfaces, cond-mat/9805366 (1998).
Pul97
W.J. Pullan, Genetic operators for the atomic cluster problem, Computer Physics Communications 107 (1997), 137-148.
PW70
David T. Philips and John West, The poor man's nitrogen laser, Am. J. Phys. 38 (1970), no. 5, 655-657.
PXK+00
E. Perola, K. Xu, T.M. Kollmeyer, S.H. Kaufmannand F.G. Prendergast, and Y.P. Pang, Successful virtual screening of a chemical database forfarnesyltransferase inhibitor leads, J. Med. Chem. 43 (2000), 401.
QPRH02
L. Qiu, S. A: Pabit, A. E. Roitberg, and S. J. Hagen, Smaller and faster: The 20-residue trp-cage protein folds in 4 microseconds, J. Am. Chem. Soc. 124 (2002), 12952.
Rem92
Reinhold Remmert, Funktionentheorie i, Springer Verlag, Berlin, 1992.
RKLK96
M. Rarey, B. Kramer, T. Lengauer, and G.A. Klebe, A fast flexible docking method using an incrementalconstruction algorithm, J. Mol Biol. 261 (1996), 470.
Rob99
B. Robson, Beyond proteins, Trends in Biotechnology 17 (1999), 311-315.
RS68
G.N. Ramachandran and V. Sasiskharan, N.a., Adv. Protein Chem. 23 (1968), 283-437.
RSS97
B. Rost, R. Schneider, and C. Sander, Protein fold recognition by prediction-based threading, J. Molec. Biol. 270 (1997), no. 471-480.
SB80
David S. Stephenson and Gerhard Binsch, Automated analysis of high-resolution nmrspectra. i.principles and computational strategy, J. Magn. Reson. 37 (1980), 395-407.
SBN+00
R. K. Soong, G. D. Bachard, H. P. Neves, A. G. Olkhovet, H. G. Craighead, and C. D. Montemagno, Powering an inorganic nanodevice with a biomolecular motor, Science 290 (2000), 1555-1559.
SBY97
H.-J. Mikeska S. Brehmer and Shoji Yamamoto, Low-temperature properties ofquantumantiferromagnetic chains with alternatingspins =1$and =1/2$, J. Phys. : Condes. Matter 9 (1997), 3921-3930.
Sch89
Harold A. Scheraga, Calculations of stable conformations ofpolypeptides, proteins, and protein complexes, Chemica Scripta 29A (1989), 3-13.
Sch90
H.-J. Schell, Unendliche reihen, 8. ed., B.G. Teubner Verlagsgesellschaft, Leipzig, 1990.
Sch96
James C. Schatzman, Accuracy of the discrete fourier transform andthefast fourier transform, SIAM J. Sci. Comput. 17 (1996), no. 5, 1150-1166.
SDaMR95
C. De Simone, M. Diehl, M. J"unger andP. Mutzel, and G. Reinelt, J. Stat. Phys. 80 (1995), 487, http://www.infortmatik.uni-koeln.de/ls_juenger/projects/sgs.html.
SFK91
Eugene Shakhnovich, G. Farztdinov, and A.M. Gutinand Martin Karplus, Protein folding bottlenecks: A lattice monte carlosimulation, Phys. Rev. Lett. 67 (1991), no. 12, 1665-1668.
SG89
E.I. Shakhnovich and A.M. Gutin, Formation of unique structure in polypeptidechains.theoretical investigation with the aid of areplicaapproach, Biophysical Chemistry 34 (1989), 187-199.
SG93
J. Sadowski and J. Gasteiger, From atoms and bonds to three-dimensional molecularmodels: Automatic model builders, Chem. Rev. 93 (1993), 2567.
SGK94
J. Sadowski, J. Gasteiger, and G. Klebe, Comparison of automatic three-dimensional model buildersusing 639 x-ray structures, J. Chem. Inf. Comput. Sci. 34 (1994), 1000.
Sha92
David Shalloway, Application of the renormalization grouptodetermenistic global minimization ofmolecularconformation energy functions, J. Glob. Opt. 2 (1992), 281-311.
Shu72
Bruno O. Shubert, A sequential method seeking the global maximum ofafunction, SIAM J. Numer. Anal. 9 (1972), no. 3, 379-388.
SJ94
I.H. Sloan and S. Joe, Lattice methods for multiple integration, Oxford University Press, Oxford, 1994.
SK89
Jeffrey Skolnick and Andrzej Kolinski, Computer simulations of globular protein foldingandtertiary structure, Annu. Rev. Phys. Chem. 40 (1989), 207-235.
SKC93
A.M. Steinberg, P.G. Kwiat, and R.Y. Chiao, Measurement of the single-photon tunneling time, Phys. Rev. Lett. 71 (1993), no. 5, 708-711.
SKHB97
K. T. Simons, C. Kooperberg, E. Huang, and D. Baker, J. Molec. Biol. 286 (1997), 209-225.
Sla94
Gordon Slade, Self-avoiding walks, The Mathematical Intelligencer 16 (1994), no. 1, 29-35.
SM73
Peter Schenk and Harold Metcalf, Low cost nitrogen laser design for dye laserpumping, App. Opt. 12 (1973), no. 2, 183-186.
SM98
R. Samudrala and J. Moult, J. Molec. Biol. 275 (1998), 895.
SMW03
A. Schug, H. Merlitz, and W. Wenzel, Stochastic optimization methods for structure prediction of biomolecular nanoscale systems, Nanotechnology 14 (2003), 1-7.
SNFH91
K. A. Sharp, A. Nicholls, R. Friedman, and B. Honig, Extracting hydrophobic free energies from experimental data:relationship to protein folding and theoretical models, Biochemistry 30 (1991), 9686-9697.
SNPG02
C. D. Snow, H. Nguyen, V. S. Panda, and M. Gruebele, Absolute comparison of simulated and experimental protein folding dynamics, Nature 420 (2002), 102-106.
SNS84
Manfred J. Sippl, George Nemethy, and HaroldA. Scheraga, Intermolecular potentials from crstaldata. 6. determination ofemperical potentials foro-h$\cdots$o$=$c hydrogen bonds frompackingconfigurations, J. Phys. Chem. 88 (1984), 6231-6233.
Sob96
Wade R.C. Vriend G. Edelman M. Sobolev, V., Preteins 25 (1996), 120, serach for binding mode of known ligand.
SPaLFB97
P.T. Sprunger, L. Petersen, and E.W. Plummer andE. Laegsgaardand F. Besenbacher, Giant friedel oscillations on the beryllium(0001)surface, Science 275 (1997), 1764-1767.
Spi91
Murray R. Spiegel, H"ohere mathematik f"ur ingenieureundnaturwissenschaftler, McGraw-Hill, Frankfurt, 1991.
SPM93
Paul E. Smith, B. Montgomery Pettitt, and MartinKarplus, Stochastic dynamics of the alanine dipeptide using asolvent-modifiedpotential energy surface, J. Phys. Chem. 97 (1993), 6907-6913.
SR73
A. Sharke and J. Rupley, J. Molec. Biol. 79 (1973), 351.
SRK+99
K. T. Simons, I. Ruczinski, C. Kooperberg, B. Fox, C. Bystroff, and D. Baker, Proteins, SF&G 34 (1999), 82-95.
SS84
Georg E. Schulz and Ralf Heiner Schirmer, Principles of protein structure, 5. ed., Springer advanced texts in chemistry, Springer, New York, 1984.
SSG+98
V. Schnecke, C. A. Swanson, E.D. Getzhoff, J.A.Tainer, and L.A. Kuhn, Screening a peptidyl database for potenital ligands to proteins with side-chain felxibility, Proteins, Structure, Function, and Genetics 33 (1998), 74-87.
SSP96
Gisbert Schneider, Johannes Schuchhardt, and PaulWrede, Evolutionary optimization in multimodal searchspace, Biol. Cyber. 74 (1996), 203-207.
SSR02
C. Simmerling, B. Stockbrine, and A. Roitberg, All-atom strucutre prediction and folding simulations of a stable protein, J. Am. Chem. Soc. 124 (2002), 11258.
ST96
David N. Schramm and Michael S. Turner, Deuteronomy and numbers, Nature 381 (1996), 193-194.
ST97
R. Salazar and R. Toral, Simulated annealing using hybrid monte carlo, cond-mat/9706051 (1997).
Sta93
Joel Stavans, The evolution of cellular structures, Rep. Prog. Phys. 56 (1993), 733-789.
SWB02
J. Schonbrunn, W. J. Wedemeyer, and D. Baker, Protein structure prediction in 2002, Curr. Op. Struc. Biol. 12 (2002), 348-352.
Tea01
IBM Blue Gene Team, Blue gene: A vision for protein science unsing a petaflop supercomuter, IBM Systems Journal 40 (2001), 310.
TFB96
David Tytler, Xiao-Ming Fan, and Scott Burles, Cosmologixal baryon density derived from thedeuteriumabundance at redshift =3.57$, Nature 381 (1996), 207-209.
Thi97a
M.J. Thill, A new old algorithm, entroy sampling, and/orgettingin and out of energy minima, cond-mat/9703233 (1997).
Thi97b
D. Thirumalai, From minimal models to real proteins: Time scalesforprotein folding kinetics, J. Phys. I France 5 (1997), 1457-1467.
TKW97
D. Thirumalai, D.K. Klimov, and S.A. Woodson, Kinetic partitioning mechanism as a unifying themeinthe folding of biomolecules, cond-mat/9704067 (1997).
ttRG73
Introduction to the Renormalization Group, Shang-keng ma, Rev. Mod. Phys 45 (1973), no. 4, 589-614.
Tv89
Aimo Törn and Antanas Zilinskas, Global optimization, Lecture Notes in Computer Science, no. 350, Springer Verlag, Berlin;Heidelberg;New York;London;Paris;Tokyo, 1989.
TvRaOSW96
M.C. Tesi and E.J. Lanse van Rensburg andE. Orlandiniand S.G. Whittington, Monte carlo study of the interactingself-avoidingwalk model in three dimensions, J. Stat. Phys. 82 (1996), 155-181.
TW96
D. Thirumalai and S.A. Woodson, Kinetics of folding of proteins and rna, Acc. Chem. Res. 29 (1996), 433-439.
uHZ97
K. Weise und H. Zhang, Uncertainty treatment in monte carlo simulation, J. Phys. A : Math. Gen. 30 (1997), 5971-5980.
UM93
R. Unger and J. Moult, J. Molec. Biol. 231 (1993), 75.
UNR93
C.J. Umrigar, M.P. Nightingale, and K.J. Runge, A diffusion monte carlo algorithm with verysmalltime-step errors, J. Chem. Phys. 99 (1993), 2865-2890.
USWFvGT97
P. Ulrich, W. Scott, W.F. W. F. van Gunsteren, and A. E. Torda, Protein structure prediction forcefields: Paramterization with quasi newtonian dynamics, Proteins, SF&G 27 (1997), 367-384.
vaJB92
Ivan Cernušak and Sullivan Beck andRodney J. Bartlett, Potential energy surface of borazirene (hcnbh), J. Phys. Chem. 96 (1992), 10284-10289.
Ved88
Angelo Vedani, Yeti: An interactive molecular mechanics programforsmall-molecule protein complexes, J. Comp. Chem. 9 (1988), no. 3, 269-280.
vGB82
W.F. van Gunsteren and H.J.C. Berendsen, Algorithms for brownian dynamics, Molecular Physics 3 (1982), 637.
vGLTT94
W.F. van Gunsteren, F. J. Luque, D. Timms, and A.E. Troda, Ann. Rev. Biophys. and Biomol. Struct. 23 (1994), 847.
VKE97
Michele Vendruscolo, Edo Kussell, and EytanDomany, Recovery of protein structure from contact maps, Folding and Design 2 (1997), 295-306.
vLA87
P.J.M. van Laarhoven and E.H.L. Aarts, Simulated annealing: Theory and applications, Mathematics and Its Applications, Kluwer, Dordrecht, 1987.
VLC83
J. N. Varghese, W. G. Laver, and P. M. Coleman, Nature 303 (1983), 35.
VNS94
M. Vasquez, G. Nemethy, and H.A. Scheraga, Chem. Rev. 94 (1994), 2138-2239.
Vog96
Erich Vogt, Elementary derivation of kepler's laws, Am. J. Phys. 64 (1996), no. 4, 392-396.
WAH96
Franz Josef Weiper, Joachim Ankerhold, and HermannGrabert, Exact and semicalssical density matrix of a particlemoving in abarrier potential with bound states, chem-ph/9602002 (1996).
Wal89a
David J. Wales, Finding saddle points for clusters, J. Chem. Phys. 91 (1989), no. 11, 7002-7010.
Wal89b
Rolf Walter, Differentialgeometrie, 2. ed., BI-Wissenschaftsverlag, Mannheim;Wien;Z"urich, 1989.
Wal97
Gordon Walker, One of our planets is missing, Nature 385 (1997), 775-776.
Wal01
C. Walsh, Enabling the chemistry of life, Nature 409 (2001), 226.
WD97
D. J. Wales and J. P.K. Doyle, JPC 101 (1997), 5111.
WH99
W. Wenzel and K. Hamacher, Stochastic tunneling approach for global optimization of complex potential energy landscapes, Phys. Rev. Lett. 82 (1999), 3003.
Wil
Kenneth G. Wilson, Problems in physics with many scales of length, Scientific American, 158-179.
Wil75
to3em, The renormalization group: Critical phenomena andthekondo problem, Rev. Mod. Phys. 47 (1975), no. 4, 773-838.
WMRS74
P.K. Warne, F.A. Momany, S. V. Rumball, and H.A. Scheraga, Biochemistry 16 (1974), 768-782.
WMW98
D. Wales, M.A. Mille, and T.R. Walsh, Nature 394 (1998), 758.
WRJ96
W. Welch, J. Ruppert, and A.N. Jain, Hammerhead: fast, fully automated docking of flexibleligands to protein binding sites, Chem. Biol. 3 (1996), 449.
WS99
D.J. Wales and H.A. Scheraga, Global optimization of clusters, crystals and biomolecules, Science 285 (1999), 1368.
WSaG66
W.T. Walter, N. Solimene, and M. Piltch andG. Gould, 6c3-efficient pulsed gas discharge lsers, IEEE Journal of Quantum Electronics QE-2 (1966), no. 9, 474-479.
WSM98
W.P. Walters, M.T. Stahl, and M.A. Murcko, Virtual screening -- an overview, Drug Discovery Today 3 (1998), 160.
Wu94
Zhijun Wu, The effectiv energy transformation scheme as aspecialcontinuation approach to global optimizationwithapplication to molecular conformation, Preprint MCS-P442-0694 Argonne National Laboratory, Illinois (1994).
WV85
L.T. Wille and J. Vennik, Computational complexity of theground-statedetermination of atomic clusters, J. Phys. A: Math. Gen. 18 (1985), L419-L422.
WW88
et.al. W. Weiss, Nature 333 (1988), 426.
WW97
David J. Wales and Tiffany R. Walsh, Theoretical study of the water tetramer, J. Chem. Phys. 106 (1997), no. 17, 7193-7207.
WW98
T. R. Walsh and D. Wales, JCP 109 (1998), 6691.
WWMCF00
E. S. Withers-Ward, T.D. Mueller, I.S. Chen, and J. Feigon, Biochemical and structural analysis of theinteraction between the uba(2) domain of the dna repair protein hhr23a and hiv-1 vpr, Biochemistry 39 (2000), 14103, 1F4I.
WWS92a
R.J. Wawak, M.M. Wimmer, and Harold A. Scheraga, Application of the diffusion equation method ofglobaloptimization to water clusters, J. Phys. Chem. 96 (1992), 5138-5145.
WWS92b
to3em, Application of the diffusion equation method ofglobaloptimization to water clusters, J. Phys. Chem. 96 (1992), 5138-5145.
YLE95
Liu Yong, Kang Lishan, and D.J. Evans, The annealing evolution algorithm asfunctionoptimizer, Parall. Comp. 21 (1995), 389-400.
YNY+01
R. Yasuda, H. Noji, M. Yoshida, K. Kinosita, and H. Itoh, Resolution of distinct rotational substeps by submillisecond kinetic analysis of f1-atpase, Nature 410 (2001), 898-904.
Zak70
V. V. Zakharov, The method of integral smoothing in many-extremalandstochastic problems, Engineer. Cyber. 4 (1970), 637-642.
Zei97
Yehuda Zeiri, Study of the lowest energy structure ofatomicclusters using a genetic algorithm, Comp. Phys. Comm. 103 (1997), 28-42.
ZK99
Y. Zhou and M. Karplus, Folding a model three helix bundle protein: thermodynamic and kinetic analysis, J. Molec. Biol. 293 (1999), 917.