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.
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- G. F. M. Beenker, T. Claasen, and P. W. C. Hermes, Philips J. Res. 40 (1985), 289.
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- 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.
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- 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.
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- 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.
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- 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.
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- to3em, Group theory of harmonic oscillators(ti). theintegrals of motion for thequadrupole-quadrupoleinteraction, Nucl. Phys. 23 (1961), 177-199.
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- 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.
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- BS87
- Arno Br"uning and Karlheinz Spallek, Zahl und zuordnung 9, Schroedel Schulbuchverlag, 1987.
- BS88
- to3em, Zahl und zuordnung 10, Schroedel Schulbuchverlag, 1988.
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- 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.
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- 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
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- BWF+00
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- CA96
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- CBaV+98
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- 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
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- 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
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- 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
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- DW97
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- DW98a
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- DW98c
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- ea57
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