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References 627
[65] G. Arya, Q. Zhang, and T. Schlick. Flexible histone tails in a new mesoscopic
oligonucleosome model. Biophys. J., 91:133–150, 2006.
[66] K. Ashrafi, F. Y. Chang, J. L. Watts, A. G. Fraser, R. S. Kamath, J. Ahringer, and
G. Ruvkun. Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory
genes. Nature, 421:268–272, 2003.
[67] A. Askar, B. Space, and H. Rabitz. Subspace method for long time scale molecular
dynamics. J. Phys. Chem., 99:7330–7338, 1995.
[68] J. F. Atkins and R. Gesteland. The 22nd amino acid. Science, 296:1409–1410,
2002.
[69] P. Auffinger, S. Louise-May, and E. Westhof. Multiple molecular dynamics sim-
ulations of the anticodon loop of rRNA
Asp
in aqueous solution with counterions.
J. Amer. Chem. Soc., 117:6720–6726, 1995.
[70] P. Auffinger, S. Louise-May, and E. Westhof. Molecular dynamics simulations of
the anticodon hairpin of tRNA
Asp
. Structuring effects of C–H···O hydrogen bonds
and long-range hydration forces. J. Amer. Chem. Soc., 118:1181–1189, 1996.
[71] P. Auffinger and E. Westhof. Molecular dynamics simulations of nucleic acids. In
P. von Rag u ´e Schleyer (Editor-in Chief), N. L. Allinger, T. Clark, J. Gasteiger, P. A.
Kollman, and H. F. Schaefer, III, editors, Encyclopedia of Computational Chem-
istry, volume 3, pages 1628–1639. John Wiley & Sons, West Sussex, England,
1998.
[72] P. Auffinger and E. Westhof. Simulations of the molecular dynamics of nucleic
acids. Curr. Opin. Struct. Biol., 8:227–236, 1998.
[73] P. Auffinger and E. Westhof. RNA solvation: A molecular dynamics simulation
perspective. Biopolymers, 56:266–274, 2001.
[74] M. S. Babcock and W. K. Olson. The effect of mathematics and coordinate system
on comparability and “dependencies” of nucleic acid structure parameters. J. Mol.
Biol., 237:98–124, 1994.
[75] D. Backowies and W. Thiel. Hybrid models for combined quantum mechanical
and molecular mechanical approaches. J. Phys. Chem., 100:10580–10594, 1996.
[76] S. Bagheri and M. Kashani-Sabet. Ribozymes in the age of molecular therapeutics.
Curr. Mol. Med., 4:489–506, 2004.
[77] I. Bahar, A. R. Atilgan, and B. Erman. Direct evaluation of thermal fluctuations in
proteins using a single-parameter harmonic potential. Fold. Des., 2:173–181, 1997.
[78] S.D. Baird, M. Turcotte, R.G. Korneluk, and M. Holcik. Searching for IRES. RNA,
12:1755–1785, 2006.
[79] D. Baker and A. Sali. Protein structure prediction and structural genomics. Science,
294:93–96, 2001.
[80] N. Baker, M. Holst, and E. Wang. Adaptive multilevel finite element solution of
the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in
biomolecular systems. J. Comput. Chem., 21:1343–1352, 2000.
[81] N. Baker, D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon. Electrostatics of
nanosystems: Application to microtubules and the ribosome. Proc. Natl. Acad. Sci.
USA, 98:10037–10041, 2001.
[82] Y Bakhtin and C. E. Heitche. Large deviations of random trees. J. Stat. Phys.,
132:551–560, 2008.
628 References
[83] D. Baltimore. The preoccupations of twenty-first-century biology. In A. H. Zewail,
editor, Physical Biology: From Atoms to Medicine, pages 1–6. Imperial College
Press, London, UK, 2008.
[84] J. Balzarini and L. V Damme. Microbicide drug candidates to prevent HIV
infection. The Lancet, 369:787–797, 2007.
[85] N. Ban, P. Nissen, J. Hansen, P. B. Moore, and T. A. Steitz. The complete atomic
structure of the large ribosomal subunit at 2.4
˚
A resolution. Science, 289:905–920,
2000.
[86] P. Ban ´aˇs, P. Jureˇcka, N. G. Walter, J.
ˇ
Sponer, and M. Otyepka. Theoretical studies
of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and
QM. Methods, 49:202–216, 2009.
[87] L. Banci, W. Baumeister, U. Heinemann, G. Schneider, I. Silman, D. I Stuart, and
J. L. Sussman. An idea whose time has come. [A response to an idea whose time
has gone by G. A. Petsko]. Genome Biol., 8:107, 2007.
[88] Y. Bao, C. L. White, and K. Luger. Nucleosome core particles containing a
poly(dA•dT) sequence element exhibit a locally distorted DNA structure. J. Mol.
Biol., 361:617–624, 2006.
[89] D. Barash, X. Qian, L. Yang, and T. Schlick. Inherent speedup limitations in
multiple-timestep/particle-mesh-Ewald algorithms. J. Comput. Chem., 24:77–88,
2003.
[90] J. Barnes and P. Hut. A hierarchical O(N log N) force-calculation algorithm.
Nature, 324:446–449, 1986.
[91] D. Barouch. Challenges in the development of an HIV-1 vaccine. Nature, 455:
613–619, 2008.
[92] E. Barth, K. Kuczera, B. Leimkuhler, and R. D. Skeel. Algorithms for constrained
molecular dynamics. J. Comput. Chem., 16:1192–1209, 1995.
[93] E. Barth, M. Mandziuk, and T. Schlick. A separating framework for increasing
the timestep in molecular dynamics. In W. F. van Gunsteren, P. K. Weiner, and
A. J. Wilkinson, editors, Computer Simulation of Biomolecular Systems: Theoreti-
cal and Experimental Applications, volume III, chapter 4, pages 97–121. ESCOM,
Leiden, The Netherlands, 1997.
[94] E. Barth and T. Schlick. Extrapolation versus impulse in multiple-timestepping
schemes: II. Linear analysis and applications to Newtonian and Langevin
dynamics. J. Chem. Phys., 109:1632–1642, 1998.
[95] E. Barth and T. Schlick. Overcoming stability limitations in biomolecular dynam-
ics: I. Combining force splitting via extrapolation with Langevin dynamics in
LN.
J. Chem. Phys., 109:1617–1632, 1998.
[96] D. Bashford and D. A. Case. Generalized Born models of macromolecular
solvation effects. Ann. Rev. Phys. Chem., 51:129–152, 2000.
[97] P. Batcho, D. A. Case, and T. Schlick. Optimized particle-mesh Ewald /
multiple-timestep integration for molecular dynamics simulations. J. Chem. Phys.,
115:4003–4018, 2001.
[98] P. Batcho and T. Schlick. New splitting formulations for lattice summations.
J. Chem. Phys., 115:8312–8326, 2001.
References 629
[99] P. Batcho and T. Schlick. Special stability advantages of position Verlet over
velocity Verlet in multiple-timestep integration. J. Chem. Phys., 115:4019–4029,
2001.
[100] A. D. Bates and A. Maxwell. DNA Topology. In Focus. Oxford University Press,
New York, NY, 1993.
[101] R. T. Batey and J. A. Doudna. The parallel universe of RNA folding. Nature Struc.
Biol., 5:337–340, 1998.
[102] R. T. Batey, R. P. Rambo, and J. A. Doudna. Tertiary motifs in RNA structure and
folding. Angew. Chem. Int. Ed., 38:2326–2343, 1999.
[103] W. R. Bauer and C. J. Benham. The free energy, enthalpy, and entropy of native and
of partially denatured closed circular DNA. J. Mol. Biol., 234:1184–1196, 1993.
[104] C. G. Baumann, S. B. Smith, V. A. Bloomfield, and C. Bustamante. Ionic effects on
the elasticity of single DNA molecules. Proc. Natl. Acad. Sci. USA, 94:6185–6190,
1997.
[105] M. D. Beachy, D. Chasman, R. B. Murphy, T. A. Halgren, and R. A. Friesner.
Accurate Ab initio quantum chemical determination of the relative energetics of
peptide conformations and assessment of empirical force fields. J. Amer. Chem.
Soc., 119:5908–5920, 1997.
[106] D. Beard and T. Schlick. Inertial stochastic dynamics: I. long-timestep methods for
langevin dynamics. J. Chem. Phys., 112:7313–7322, 2000.
[107] D. Beard and T. Schlick. Inertial stochastic dynamics: II. influence of inertia on
slow kinetic properties of supercoiled DNA. J. Chem. Phys., 112:7323–7338,
2000.
[108] D. Beard and T. Schlick. Computational modeling predicts the structure and
dynamics of the chromatin fiber. Structure, 9:105–114, 2001.
[109] D. Beard and T. Schlick. Modeling salt-mediated electrostatics of macromolecules:
The algorithm DiSCO (Discrete Charge Surface Charge Optimization) and its
application to the nucleosome. Biopolymers, 58:106–115, 2001.
[110] J. C. Beauchamp and N. W. Isaacs. Methods for X-ray diffraction analysis of
macromolecular structures. Curr. Opin. Chem. Biol., 3:525–529, 1999.
[111] O. M. Becker, D. S. Dhanoa, Y. Marantz, D. Chen, S. Shacham, S. Cheruku,
A. Heifetz, P. Mohanty, M. Fichman, and A. Sharadendu. An integrated in sil-
ico 3D model-driven discovery of a novel, potent, and selective amidosulfonamide
5-HT1A agonist (PRX-00023) for the treatment of anxiety and depression. J. Med.
Chem., 49:3116–3135, 2006.
[112] D. Beglov and B. Roux. Dominant solvations effects from the primary shell
of hydration: Approximation for molecular dynamics simulations. Biopolymers,
35:171–178, 1994.
[113] D. Beglov and B. Roux. Finite representation of an infinite bulk system: Sol-
vent boundary potential for computer simulations. J. Chem. Phys., 100:9050–9063,
1994.
[114] D. Beglov and B. Roux. Numerical solutions of the hypernetted chain equation for
a solute of arbitrary geometry in three dimensions. J. Chem. Phys., 103:360–364,
1995.
630 References
[115] J. Bella, B. Brodsky, and H. M. Berman. Hydration structure of a collagen peptide.
Structure, 3:893–906, 1995.
[116] G. Benedetti and S. Morosetti. A graph-topological approach to recognition of
pattern and similarity in RNA secondary structures. Biophys. Chem., 59:179–184,
1996.
[117] Y. Benenson, B. Gil, U. B.-D., R. Adar, and E. Shapiro. An autonomous molecular
computer for logical control of gene expression. Nature, 429:423–429, 2004.
[118] H. A. Benjamin and N. R. Cozzarelli. DNA-directed synapsis in recombination:
Slithering and random collision of sites. Proc. R. A. Welch Found. Conf. Chem.
Res., 29:107–126, 1986.
[119] K. R. Benjamin, A. P. Abola, R. Kanaar, and N. R. Cozzarelli. Contributions of su-
percoiling to Tn3 resolvase and phage Mu Gin site-specific recombination. J. Mol.
Biol., 256:50–65, 1996.
[120] D. Bensimon, A. Simon and. A. Chiffaudel, V. Croquette, and A. Bensimon.
Alignment and sensitive detection of DNA by a moving interface. Science,
265:2096–2098, 1994.
[121] H. J. C. Berendsen. A glimpse of the holy grail. Science, 282:642–643, 1998.
[122] H. J. C. Berendsen. Simulating the Physical World: Hierarchical Modeling from
Quantum Mechanics to Fluid Dynamics. Cambridge University Press, Cambridge,
UK, 2007.
[123] H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R.
Haak. Molecular dynamics with coupling to an external bath. J. Chem. Phys.,
81:3684–3690, 1984.
[124] H. J. C. Berendsen, D. van der Spoel, and R. van Drunen. GROMACS: A message-
passing parallel molecular dynamics implementation. Comput. Phys. Comm.,
91:43–56, 1995.
[125] H. M. Berman. Hydration of DNA: Take 2. Curr. Opin. Struct. Biol., 4:345–350,
1994.
[126] H. M. Berman. Crystal studies of B-DNA: The answers and the questions.
Biopolymers, 44:23–44, 1997.
[127] H. M. Berman, W. K. Olson, D. L. Beveridge, J. Westbrook, A. Gelbin, T. Demeny,
S.-H. Hsieh, A. R. Srinivasan, and B. Schneider. The nucleic acid database: A com-
prehensive relational database of three-dimensional structures of nucleic acids.
Biophys. J., 63:751–759, 1992.
[128] H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig,
I. N. Shindyalov, and P. E. Bourne. The protein data bank. Nucleic Acids Res.,
28:235–242, 2000.
[129] B. J. Berne and J. E. Straub. Novel methods of sampling phase space in the
simulation of biological systems. Curr. Opin. Struct. Biol., 7:181–189, 1997.
[130] S. Bern`eche and B. Roux. Energetics of ion conduction through the K
+
channel.
Nature, 414:73–77, 2001.
[131] R.S.Berry,S.A.Rice,andJ.Ross.Physical Chemistry. Wiley, New York, NY,
1980.
[132] R. B. Best, N.-V. Buchete, and G. Hummer. Are current molecular dynamics force
fields too helical? Biophys. J., 95:L07–L09, 2008.
References 631
[133] D. L. Beveridge, G. Barreiro, K. S. Byun, D. A. Case, T. E. Cheatham, III,
S. B. Dixit, E. Giudice, F. Lankas, R. Lavery, J. H. Maddocks, R. Osman,
E. Seibert, H. Sklenar, G. Stoll, K. M. Thayer, P. Varnai, and M. A. Young. Molec-
ular dynamics simulations of the 136 unique tetranucleotide sequences of DNA
oligonucleotides. I: Research design and results on d(C
p
G) steps. Biophys. J.,
87:3799–3813, 2004.
[134] J. J. Biesiadecki and R. D. Skeel. Dangers of multiple-time-step methods.
J. Comput. Phys., 109:318–328, 1993.
[135] M. Bixon, H. Dekker, J. D. Dunitz, E. Eser, S. Lifson, C. Mosselman, J. Sicher,
and M. Svoboda. Structural and strain-energy consequences of “intra-annular”
substitution in the cyclodecane ring. Chem. Commun., pages 360–362, 1967.
[136] P. Bjelkmar, P. S. Niemel¨a, I. Vattulainen, and E. Lindahl. Conformational changes
and slow dynamics through microsecond polarized atomistic molecular simulation
of an integral Kv1.2 ion channel. PLoS Comp. Biol., 5:e1000289, 2009.
[137] G. M. Blackburn and M. J. Gait, editors. Nucleic Acids in Chemistry and Biology.
Oxford University Press, New York, NY, 1990.
[138] V. A. Bloomfield. DNA condensation by multivalent cations. Biopolymers,
44:269–282, 1997.
[139] V. A. Bloomfield, D. M. Crothers, and I. Tinoco, Jr. Nucleic Acids: Structures,
Properties, and Functions. University Science Press, New York, NY, 2000.
[140] J. Board, A. John, Z. S. Hakura, W. D. Elliott, and W. T. Rankin. Scalable vari-
ants of multipole-accelerated algorithms for molecular dynamics applications.
In Proceedings, Seventh SIAM Conference on Parallel Processing for Scientific
Computing, pages 295–300, Philadelphia, PA, 1995. SIAM.
[141] J. Board, A. John, C. W. Humphres, C. G. Lambert, W. T. Rankin, and A. Y.
Toukmaji. Ewald and multipole methods for periodic N-body problems. In
Proceedings, Eighth SIAM Conference on Parallel Processing for Scientific
Computing, Philadelphia, PA, 1997. SIAM. CD-ROM.
[142] J. A. Board, Jr., J. W. Causey, T. F. Leathrum, Jr., A. Windemuth, and K. Schulten.
Accelerated molecular dynamics simulations with the parallel fast multiple
algorithm. Chem. Phys. Lett., 198:89–94, 1992.
[143] J. A. Board, Jr., L. V. Kal´e, K. Schulten, R. D. Skeel, and T. Schlick. Modeling
biomolecules: Larger scales, longer durations. IEEE Comput. Sci. Eng., 1:19–30,
Winter 1994.
[144] M. D. Bojin and T. Schlick. A quantum mechanical investigation of possible
mechanisms for the nucleotidyl transfer reaction catalyzed by DNA polymerase
β. J. Phys. Chem. B, 111:11244–11252, 2007.
[145] T. C. Boles, J. H. White, and N. R. Cozzarelli. Structure of plectonemically
supercoiled DNA. J. Mol. Biol., 213:931–951, 1990.
[146] P. G. Bolhuis. Rare events via multiple reaction channels sampled by path replica
exchange. J. Chem. Phys., 129:114108, 2008.
[147] P. G. Bolhuis, D. Chandler, C. Dellago, and P. L. Geissler. Transition path sam-
pling: Throwing ropes over rough mountain passes, in the dark. Annu. Rev. Phys.
Chem, 53:291–318, 2002.
[148] M. Bon, G. Vernizzi, H. Orland, and A. Zee. Topological classification of RNA
structures. J. Mol. Biol., 379:900–911, 2008.
632 References
[149] R. Bonneau, J. Tsai, I. Ruczinski, and D. Baker. Functional inferences from blind
ab initio protein structure predictions. J. Struc. Biol., 134:186–190, 2001.
[150] S. Boresch, S. Ringhofer, P. H¨ochtl, and O. Steinhauser. Towards a better de-
scription and understanding of biomolecular solvation. Biophys. Chem., 78:43–68,
1999.
[151] S. Borman. Reducing time to drug discovery. Chem. Eng. News, 77:33–48, 1998.
[152] E. E. Borrero and F. A. Escobedo. Optimizing the sampling and staging for
simulations of rare events via forward flux sampling schemes. J. Chem. Phys.,
129:024115, 2008.
[153] J. M. Borwein and A. S. Lewis. Convex Analysis and Nonlinear Optimization.
Theory and Examples, volume 3 of Canadian Mathematical Society (CMS) Books
in Mathematics. Springer-Verlag, New York, NY, 2000.
[154] A. H. Boschitsch, M. O. Fenley, and W. K. Olson. A fast adaptive multipole algo-
rithm for calculating screened Coulomb (Yukawa) interactions. J. Comput. Phys.,
151:212–241, 1999.
[155] G. C. Boulougouris and D. Frenkel. Novel Monte Carlo scheme for systems with
short-ranged interactions. J. Chem. Phys., 122:244105, 2005.
[156] K. J. Bowers, E. Chow, H. Xu, R. O. Dror, M. P. Eastwood, B. A. Gregersen, J. L.
Klepeis, I. Kolossvary, M. A. Moraes, F. D. Sacerdoti, J. K. Salmon, Y. Shan, and
D. E. Shaw. Scalable algorithms for molecular dynamics simulations on commod-
ity clusters. In Proceedings of the 2006 ACM/IEEE Conference on Supercomputing
(SC06), Tampa, Florida, New York, 2006. ACM Press.
[157] J. U. Bowie, R. L¨uthy, and D. Eisenberg. A method to identify protein sequences
that fold into a known three-dimensional structure. Science, 253:164–170, 1991.
[158] G. R. Bowman and V. S. Pande. The roles of entropy and kinetics in structure
prediction. PLoS ONE, 4:e5840, 2009. doi:10.1371/journal.pone.0005840.
[159] D. B. Boyd. Computer-aided molecular design. In A. Kent (Executive) and
C. M. Hall (Administrative), editors, Encyclopedia of Library and Informa-
tion Science, volume 59, pages 54–84. Marcel Dekker, New York, NY, 1997.
Supplement 22.
[160] D. B. Boyd. Rational drug design: Controlling the size of the haystack. Mod. Drug
Dis., 1:41–47, 1998.
[161] S. F. Brady, K. J. Stauffer, W. C. Lumma, G. M. Smith, H. G. Ramjit, S. D.
Lewis, B. J. Lucas, S. J. Gardell, E. A. Lyle, S. D. Appleby, J. J. Cook,
M. A. Holahan, M. T. Stranieri, J. J. Lynch, Jr., J. H. Lin, I.-W. Chen, K. Vastag,
A. M. Naylor-Olsen, and J. P. Vacca. Discovery and development of the novel
potent orally active thrombin inhibitor N-(9-Hydroxy-9-fluorenecarboxy)prolyl
trans-4-Aminocyclohexylmethyl amide (L-372,460): Coapplication of structure-
based design and rapid multiple analogue synthesis on solid support. J. Med.
Chem., 41(3):401–406, 1998.
[162] R. S. Braich, N. Chelyapov, C. Johnson, P. W. K. Rothemund, and L. Adleman.
Solution of a 20-variable 3-SAT problem on a DNA computer. Science,
296:499–502, 2002.
[163] C. Branden and J. Tooze. Introduction to Protein Structure. Garland Publishing
Inc., New York, NY, second edition, 1999. (www.proteinstructure.com/).
References 633
[164] A. Brandt and A. A. Lubrecht. Multilevel matrix multiplication and fast solution
of integral equations. J. Comput. Phys., 90:348–370, 1990.
[165] P. Bratley, B. L. Fox, and L. E. Schrage. A Guide to Simulation. Springer-Verlag,
New York, NY, second edition, 1987.
[166] R. R. Breaker. Natural and engineered nucleic acids as tools to explore biology.
Nature, 432:838–845, 2004.
[167] S. E. Brenner. A tour of structural genomics. Nat. Genet., 2:801–809, 2001.
[168] S. E. Brenner, C. Chothia, and T. J. P. Hubbard. Population statistics of pro-
tein structures: Lessons from structural classifications. Curr. Opin. Struct. Biol.,
7:369–376, 1997.
[169] K. J. Breslauer, R. Frank, H. Bl¨ocker, and L. A. Marky. Predicting DNA duplex
stability from the base sequence. Proc. Natl. Acad. Sci. USA, 83:3746–3750, 1986.
[170] I. Brierley, S. Pennell, and R.J. Gilbert. Viral RNA pseudoknots: versatile motifs
in gene expression and replication. Nat. Rev. Microbiol., 5:598–610, 2007.
[171] R. Brimacombe. The bacterial ribosome at atomic resolution. Structure,
8:R195–R200, 2000.
[172] P. Brion and E. Westhof. Hierarchy and dynamics of RNA folding. Ann. Rev.
Biophys. Biomol. Struc., 26:113–137, 1997.
[173] J. E. Brody. What to serve for dinner, when dinner is on Mars. The New York Times,
pages F1–2, 19 May 1998.
[174] B. R. Brooks, C. L. Brooks, III, Jr. A. D. MacKerell, L. Nilsson, R. J. Petrella,
B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Calflisch, L. Caves,
Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera,
T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z.
Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang,
D. M. York, and M. Karplus. CHARMM: the biomolecular simulation program.
J. Comput. Chem., 30:1545–1614, 2009.
[175] B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and
M. Karplus. CHARMM: A program for macromolecular energy, minimization,
and dynamics calculations. J. Comput. Chem., 4:187–217, 1983.
[176] C. L. Brooks, III. Viewing protein folding from many perspectives. Proc. Natl.
Acad. Sci. USA, 99:1099–1100, 2002.
[177] C. L. Brooks, III. With a little help ... Nature, 420:33–34, 2002.
[178] C. L. Brooks, III, M. Karplus, and B. M. Pettitt. Proteins: A Theoretical Perspective
of Dynamics, Structure, and Thermodynamics, volume 71 of Advances in Chemical
Physics. John Wiley & Sons, New York, NY, paperback edition, 1990.
[179] C. L. Brooks, III, J. N. Onuchic, and D. J. Wales. Statistical thermodynamics:
Taking a walk on a landscape. Science, 293:612–613, 2001.
[180] A. Br¨unger, C. L. Brooks, III, and M. Karplus. Stochastic boundary conditions for
molecular dynamics simulations of ST2 water. Chem. Phys. Lett., 105:495–500,
1982.
[181]
A. T. Br¨unger, P. D. Adams, and L. M. Rice. New applications of simulated
annealing in X-ray crystallography and solution NMR. Structure, 5:325–336,
1997.
634 References
[182] Z. Bryant, M. D. Stone, J. Gore, S. B. Smith, N. R. Cozzarelli, and C. Bustamante.
Structural transitions and elasticity from torque measurements on DNA. Nature,
424:338–341, 2003.
[183] M. Bucciantini, E. Giannoni, F. Chiti, F. Baroni, L. Formigli, J. Zurdo, N. Taddei,
G. Ramponi, C. M. Dobson, and M. Stefani. Inherent toxicity of aggregates im-
plies a common mechanism for protein misfolding diseases. Nature, 416:507–511,
2002.
[184] F. Bueche. The viscoelastic properties of plastics. J. Chem. Phys., 22:603–609,
1954.
[185] U. Burkert and N. L. Allinger. Molecular Mechanics, volume 177 of American
Chemical Society Monograph. ACS, Washington D. C., 1982.
[186] A. M. Burkhoff and T. D. Tullius. The unusual conformation adopted by the
adenine tracts in kinetoplast DNA. Cell, 48:935–943, 1987.
[187] C. Bustamante. In singulo biochemistry: When less is more. Ann. Rev. Biochem.,
77:45–50, 2008.
[188] C. Bustamante, Z. Bryant, and S. B. Smith. Ten years of tension: Single-molecule
DNA mechanics. Nature, 421:423–427, 2003.
[189] C. Bustamante and D. Keller. Scanning force microscopy in biology. Physics
Today, 48:32–38, 1995.
[190] C. Bustamante, J. F. Marko, E. D. Siggia, and S. Smith. Entropic elasticity of
λ-phage DNA. Science, 265:1599–1600, 1994.
[191] E. C. Butcher, E. L. Berg, and E. J. Kunkel. Systems biology in drug discovery.
Nat. Biotech., 22:1253–1259, 2004.
[192] R. H. Byrd, P. Lu, and J. Nocedal. A limited memory algorithm for bound
constrained optimization. SIAM J. Sci. Stat. Comput., 16:1190–1208, 1995.
[193] R. H. Byrd, J. Nocedal, and R. B. Schnabel. Representations of quasi-Newton
matrices and their use in limited memory methods. Math. Prog., 63:129–156, 1994.
[194] R. H. Byrd, J. Nocedal, and C. Zhu. Towards a discrete Newton method with mem-
ory for large-scale optimization. In G. Di Pillo and F. Giannessi, editors, Nonlinear
Optimization and Applications. Plenum, 1996.
[195] C. R. Calladine and H. R. Drew. Understanding DNA. The Molecule and How It
Works. Academic Press, San Diego, CA, second edition, 1997.
[196] F. Calvo. Non-genetic global optimization methods in molecular science: An
overview. Comp. Mat. Sci., 45:8–15, 2009.
[197] C. R. Cantor and P. R. Schimmel. Biophysical Chemistry, volume 1–3. W. H.
Freeman and Company, San Francisco, 1980.
[198] P. R. Caron, M. D. Mullican, R. D. Mashal, K. P. Wilson, M. S. Su, and M. A.
Murcko. Chemogenomic approaches to drug discovery. Curr. Opin. Chem. Biol.,
5:464–470, 2001.
[199] J. M. Carothers, S. C. Oestreich, J. H. Davis, and J. W. Szostak. Informa-
tional complexity and functional activity of RNA structures. J. Amer. Chem. Soc.,
126:5130–5137, 2004.
[200] J. C. Carrington and V. Ambros. Role of microRNAs in plant and animal
development. Science, 301:336–338, 2003.
References 635
[201] A. P. Carter, W. M. Clemons, D. E. Brodersen, R. J. Morgan-Warren,
B. T. Wimberly, and V. Ramakrishnan. Functional insights from the struc-
ture of the 30S ribosomal subunit and its interactions with antibiotics. Nature,
407:340–348, 2000.
[202] D. A. Case. Normal mode analysis of protein dynamics. Curr. Opin. Struc. Biol.,
4:385–290, 1994.
[203] D. A. Case. NMR refinement. In P. von Ragu´e Schleyer (Editor-in Chief), N. L.
Allinger, T. Clark, J. Gasteiger, P. A. Kollman, and H. F. Schaefer, III, editors, En-
cyclopedia of Computational Chemistry, volume 3, pages 1866–1876. John Wiley
& Sons, West Sussex, England, 1998.
[204] D. A. Case, T. E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Jr. Merz,
A. Onufriev, C. Simmerling, B. Wang, and R. J. Woods. The Amber biomolecular
simulation programs. J. Comput. Chem., 26:1668 W1688, 2005.
[205] L. Castagnoli, M. Scarpa, M. Kokkinidis, D.W. Banner, D. Tsernoglou, and
G. Cesareni. Genetic and structural analysis of the CoIE1 Rop (Rom) protein.
Embo. J., 8:621–629, 1989.
[206] J. H. Cate, M. M. Yusupov, C. Zh. Yusupova, T. N. Earnest, and H. F. Noller. X-ray
crystal structure of 70S ribosome functional complexes. Science, 285:2095–2104,
1999.
[207] T. Caulfield and K. Burgess. Combinatorial chemistry. Focused diversity and
diversity of focus. Curr. Opin. Chem. Biol., 5:241–242, 2001.
[208] M. Cavazzana-Calvo and A. Fischer. Gene therapy for severe combined immun-
odeficiency: Are we there yet? J. Clin. Inves., 117:1456–1465, 2007.
[209] L. S. D. Caves, J. D. Evanseck, and M. Karplus. Locally accessible conforma-
tions of proteins: Multiple molecular dynamics simulations of crambin. Prot. Sci.,
7:649–666, 1998.
[210] T. R. Cech. The ribosome is a ribozyme. Science, 289:878–879, 2000.
[211] L. Cerchia and V. De Franciscis. Noncoding RNAs in cancer medicine. J. Biomed.
Biotechnol., 2006:73104, 2006.
[212] M. R. Chance, A. R. Bresnick, S. K. Burley, J.-S. Jiang, C. D. Lima, A. Sali,
S. C. Almo, J. B. Bonanno, J. A. Buglino, S. Boulton, H. Chen, N. Eswar, G. He,
R. Huang, V. Ilyin, L. McMahan, U. Pieper, S. Ray, M. Vidal, and L. K. Wang.
Structural genomics: A pipeline for providing structures for the biologist. Prot.
Sci., 11:723–738, 2002.
[213] D. Chandler. Introduction to Modern Statistical Mechanics. Oxford University
Press, New York, NY, 1987.
[214] J.-M. Chandonia and S. E. Brenner. The impact of structural genomics: Eexpecta-
tions and outcomes. Science, 311:347–351, 2006.
[215] R. Chandrasekaran and S. Arnott. The structure of B-DNA in oriented fibers.
J. Biomol. Struct. Dynam., 13:1015–1027, 1996.
[216] T. E. Cheatham, III. Simulation and modeling of nucleic acid structure, dynamics
and interactions. Curr. Opin. Struct. Biol., 14:360–367, 2004.
[217] T. E. Cheatham, III. Molecular modeling and atomistic simulation of nucleic acids.
Ann. Rev. Comp. Chem., 1:75–89, 2005.
636 References
[218] T. E. Cheatham, III, P. Cieplak, and P. A. Kollman. A modified version of the cornel
et al. force field with improved sugar pucker phases and helical repeat. J. Biomol.
Struct. Dynam., 16:845–862, 1999.
[219] T. E. Cheatham, III and P. A. Kollman. Observation of the A-DNA to B-DNA
transition during unrestrained molecular dynamics in aqueous solution. J. Mol.
Biol., 259:434–444, 1996.
[220] T. E. Cheatham, III, J. L. Miller, T. Fox, T. A. Darden, and P. A. Kollman. Molec-
ular dynamics simulations of solvated biomolecular systems: The particle mesh
Ewald method leads to stable trajectories of DNA, RNA, and proteins. J. Amer.
Chem. Soc., 117:4193–4194, 1995.
[221] T. E. Cheatham, III and M. A. Young. Molecular dynamics simulation of nucleic
acids: Successes, limitations, and promise. Biopolymers, 56:232–256, 2001.
[222] Y. Chebaro, X. Dong, R. Laghaei, P. Derreumaux, and N. Mousseau. Replica
exchange molecular dynamics simulations of coarse-grained proteins in implicit
solvent. J. Phys. Chem. B., 113:267–274, 2009.
[223] J. Chen and C. L. Brooks, III. Implicit modeling of nonpolar solvation for simu-
lating protein folding and conformational transitions. Phys. Chem. Chem. Phys.,
10:471–481, 2008.
[224] L. Chen and M. W. Deem. Monte Carlo methods for small molecule high-
throughput experimentation. J. Chem. Inf. Comput. Sci., 41:950–957, 2001.
[225] S.-J. Chen. RNA folding: Conformational statistics, folding kinetics, and ion
electrostatics. Ann. Rev. Biphys., 37:197–214, 2008.
[226] W. W. Chen, J. S. Yand, and E. Shakhnovich. A knowledge-based move set for
protein folding. Prot. Struc. Funct. Bioinf., 66:682–688, 2007.
[227] Z. Chen, Y. Li, E. Chen, D. L. Hall, P. L. Darke, C. Culberson, J. A. Shafer, and
L. C. Kuo. Crystal structure at 1.9-
˚
A resolution of human immunodeficiency (HIV)
II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV
proteases. J. Biol. Chem., 269:26344–26348, 1994.
[228] D. Y. Cherny, B. P. Belotserkovskii, M. D. Frank-Kamenetskii, M. Egholm,
O. Buchardt, R. H. Berg, and P. E. Nielsen. DNA unwinding upon strand-
displacement binding of a thymine-substituted polyamide to double-stranded
DNA. Proc. Natl. Acad. Sci. USA, 90:1667–1670, 1993.
[229] S. Chew, P. Chen, N. Link, K. Galindo, K. Pogue, and J. Abrams. Genome-wide
silencing in Drosophila captures conserved apoptotic effectors. Nature, 460:123–
127, 2009.
[230] D. N. Chin, F. Sussman, H. M. Chun, and R. Czerminski. A simple solvation model
along with a multibody dynamics strategy MBO(N)D produces stable DNA sim-
ulations that are faster than traditional atomistic methods. Mol. Sim., 24:449–463,
2000.
[231] G. Chirico and J. Langowski. Calculating hydrodynamic properties of DNA
through a second-order Brownian dynamics algorithm. Macromolecules, 25:769–
775, 1992.
[232] G. Chirico and J. Langowski. Kinetics of DNA supercoiling studied by Brownian
dynamics simulation. Biopolymers, 34:415–433, 1994.
[233]
G. Chirico and J. Langowski. Brownian dynamics simulations of supercoiled DNA
with bent sequences. Biophys. J., 71:955–971, 1996.