Schlick Group Publication List


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Philip Morris External Research Program
Alfred P. Sloan Foundation
American Association of University Women Educational Foundation
American Chemical Society
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Howard Hughes Medical Institute
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National Institute of General Medical Sciences
National Institutes of Health
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New York University
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Mathematical and physical sciences
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  		1. Y. Xin, G. Quarta, H.H. Gan, and T. Schlick, "Estimating the fraction of noncoding RNAs in mammalian transcriptomes.", Bioinformatics and Biology Insights, 2:77-95(2008)

  		2. N. Kim, J.S. Shin, S. Elmetwaly, H.H. Gan and T. Schlick, "RAGPOOLS: RNA-As-Graph-Pools A Web Server for Assisting the Design of Structured RNA Pools for In Vitro Selection", Bioinformatics, doi:10.1093/bioinformatics/btm439(2007)

  		3. M.D. Bojin and T. Schlick, "A quantum mechanical investigation of possible mechanisms for the nucleotidyl transfer reaction catalyzed by DNA polymerase ", J. Phys. Chem. B, 111(38),11244-11252,(2007)

  		4. I.L. Alberts, Y. Wang, T. Schlick, "DNA polymerase catalysis: are different mechanisms possible?" , J Am Chem Soc, 129(36):11100-10(2007)

  		5. N. Kim, H. H. Gan, and T. Schlick, "A Computational Proposal for Designing Structured RNA Pools for in Vitro Selection of RNAs", RNA, 13:478-92(2007)

  		6. Y. Wang, S. Reddy, W. Beard, S. Wilson, and T. Schlick, "Differing Conformational Pathways Before and After Chemistry for Insertion of dATP vs. dCTP Opposite 8-oxoG in DNA Polymerase Beta", Biophys. J.,92:3063-3070 (2007)

  		7. Y. Wang and T. Schlick, "Distinct Energetics and Closing Pathwasys for DNA Polymerase Beta with 8-oxoG Template and Different Incoming Nucleotides" BMC Structural Biology, 7:7 (2007)

  		8. G. Arya and T. Schlick, "Efficient Global Biopolymer Sampling with End-Transfer Configurational Bias Monte Carlo" J. Chem. Phys., 126:044107 (2007)

  		9. R. Radhakrishnan and T. Schlick, "Correct and Incorrect Nucleotide Incorporation Pathways in DNA Polymerase Betas" Biochem. Biophys. Res. Comm., 350:521-529 (2006)

  		10. M. Foley, K. Arora, and T. Schlick, "Sequential Side-chain Residue Motions Transform the Binary into the Ternary State of DNA Polymerase Lambda" Biophys. J., 91:3182-3195 (2006)

  		11. G. Arya and T. Schlick, "Role of Histone Tails in Chromatin Folding Revealed by a New Mesoscopic Oligonucleosome Model", PNAS, 103:16236-16241 (2006)

  		12. R. Radhakrishnan, K. Arora, Y. Wang, W. Beard, S. Wilson, and T. Schlick, "Regulation of DNA Repair Fidelity by Molecular Checkpoints: "Gates" in DNA Polymerase Beta's Substrate Selection", Biochem., 45:15142-15156 (2006)

  		13. G. Arya, Q. Zhang, and T. Schlick, "Flexible Histone Tails in a New Mesopscopic Model of Oligonucleosomes", Biophys. J., 91:133-150 (2006)

  		14. Q. Zhang and T. Schlick, "Stereochemistry and Position-Dependent Effects of Carcinogens on TATA/TBP Binding", Biophys. J., 90:1865-1877 (2006)

  		15. T. Schlick, "RNA: The Cousin Left Behind Becomes a Star", in Computational Studies of DNA and RNA, pp.259-281, J. Sponer and F. Lankas, Editors, Springer Verlag, Dordrecht, The Netherlands (2006)

  		16. B. Sampoli Benitez, K. Arora, and T. Schlick, "In Silico Studies of the African Swine Fever Virus DNA Polymerase X support an Induced-fit Mechanism", Biophys. J., 90:42-56 (2006)

  		17. Y. Wang, K. Arora, and T. Schlick, "Subtle but Variable Conformational Rearrangements in the Replication Cycle of Sulfolobus solfactarius P2 DNA polymerase IV (Dpo4) May Accommodate Lesion Bypass", Prot. Sci., 15:135-151 (2006)

  		18. K. Arora, W. A. Beard, S. H. Wilson, and T. Schlick, "Mismatch Induced Conformational Distortions in Polymerase Support an Induced-Fit Mechanism for Fidelity", Biochem., 44:13328-13341 (2005)

  		19. U. Laserson, H. H. Gan, and T. Schlick, "Predicting Candidate Genomic Sequences that Correspond to Synthetic Functional RNA Motifs", Nuc. Acids Res., 33:6057-6069 (2005)

  		20. U. Laserson, H. H. Gan, and T. Schlick, "Exploring the Connection Between Synthetic and Natural RNAs in Genomes Via a Novel Computational Approach", in Advances in Algorithms for Macromolecular Simulation, Proceedings of the Fourth International Workshop on Algorithms for Macromolecular Modelling, Leicester, UK, August 2004, C. Chipot, R. Elber, A. Laaksonen, B. Leimkuhler, A. Mark, T. Schlick, R.D. Skeel, C. Schuette, Editors, Lecture Notes in Computational Science and Engineering, Vol. 49, pp. 35-56, Springer-Verlag, Berlin (2005)

  		21. J. Gevertz, H. H. Gan, and T. Schlick, " In Vitro RNA Random Pools are Not Structurally Diverse: A Computational Analysis", RNA, 11:853-863 (2005)

  		22. R. Radhakrishnan and T. Schlick, "Fidelity Discrimination in DNA Polymerase : Differing Closing Profiles for a Mismatched (G:A) Versus Matched (G:C) Base Pair", J. Amer. Chem. Soc., 127:13245-13252 (2005)

  		23. J. Sun, Q. Zhang, and T. Schlick, "Electrostatic Mechanism of Nucleosomal Array Folding Revealed by Computer Simulation", PNAS, 102:8180-8185 (2005)

  		24. K. Arora and T. Schlick, "Conformational Transition Pathway of Polymerase /DNA Complex Upon Binding Correct Incoming Substrate", J. Phys. Chem. B, 109:5358-5367 (2005)

  		25. T. Schlick, "The Critical Collaboration Between Art and Science: Applying an Experiment on a Bird in an Air Pump to the Ramifications of Genomics on Society", Leonardo, 38(4):323-329 (2005)

  		26. S. Pasquali, H. H. Gan, and T. Schlick, "Modular RNA Architecture Revealed by Computational Analysis of Existing Pseudoknots and Ribosomal RNAs", Nuc. Acids Res., 33:1384-1398 (2005)

  		27. N. Kim, N. Shiffeldrim, H. H. Gan, and T. Schlick, "Candidates for Novel RNA Topologies", J. Mol. Biol., 341:1129-1144 (2004)

  		28. R. Radhakrishnan and T. Schlick, "Biomolecular Free Energy Profiles by a Shooting/Umbrella Sampling Protocol, `BOLAS' ", J. Chem. Phys., 121:2436-2444 (2004)

  		29. U. Laserson, H. H. Gan, and T. Schlick, "Searching for 2D RNA Geometries in Bacterial Genomes", Proceedings of the Twentieth Annual ACM Symposium on Computational Geometry, June 9-11, New York, 373-377, ACM Press (2004)

  		30. R. Radhakrishnan and T. Schlick, "Orchestration of Cooperative Events in DNA Synthesis and Repair Mechanism Unraveled by Transition Path Sampling of DNA Polymerase 's Closing", Proc. Natl. Acad. Sci., 101:5970-5975 (2004)

  		31. L. Yang, K. Arora, W. A. Beard, S. H. Wilson, and T. Schlick, "Critical Role of Magnesium Ions in DNA Polymerase 's Closing and Active Site Assembly", J. Am. Chem. Soc., 126:8441-8453 (2004)

  		32. K. Arora and T. Schlick, "In Silico Evidence for DNA Polymerase 's Substrate-Induced Conformational Change", Biophys. J., 87:3088-3099 (2004)

  		33. K. Arora and T. Schlick, "Deoxyadenosine Sugar Puckering Pathway Simulated by the Stochastic Difference Equation Algorithm", Chem. Phys. Lett., 378:1-8 (2003)

  		34. Q. Zhang, S. Broyde, and T. Schlick, "Deformations of Promoter DNA Bound to Carcinogens Help Interpret Effects on TATA-element Structure and Activity", Phil. Trans. Roy. Soc. Lond., Series A: Mathematical, Physical & Engineering Sciences, 362: 1479-1496 (2004)

  		35. H. H. Gan, D. Fera, J. Zorn, N. Shiffeldrim, U. Laserson, N. Kim, and T. Schlick, "RAG: RNA-As-Graphs Database - Concepts, Analysis, and Features", Bioinformatics, 20: 1285-1291 (2004)

  		36. D. Fera, N. Kim, N. Shiffeldrim, J. Zorn, U. Laserson, H. H. Gan, and T. Schlick, "RAG: RNA-As-Graphs Web Resource", BMC Bioinformatics, 5:88 (2004)

  		37. J. Zorn, H. H. Gan, N. Shiffeldrim, and T. Schlick, "Structural Motifs in Ribosomal RNAs: Implications for RNA Design and Genomics", Biopolymers, 73: 340-347 (2004)

  		38. Q. Zhang, D. A. Beard, and T. Schlick, "Constructing Irregular Surfaces to Enclose Macromolecular Complexes for Mesoscale Modeling Using the Discrete Surface Charge Optimization (DiSCO) Algorithm", J. Comp. Chem., 24:2063-2074 (2003)

  		39. T. Schlick, "Engineering Teams Up with Computer-Simulation and Visualization Tools to Probe Biomolecular Mechanisms", Biophys. J., New and Notable, 85:1-4 (2003)

  		40. L. Yang, W. A. Beard, S. H. Wilson, S. Broyde, and T. Schlick, "Highly Organized but Pliant Active-site of DNA Polymerase : Compensatory Mechanisms in Mutant Enzymes Revealed by Dynamics Simulations and Energy Analysis", Biophys. J., 86: 3392-3408 (2004)

  		41. D. A. Beard and T. Schlick, "Unbiased Rotational Moves for Rigid-Body Dynamics", Biophys. J., 85:2973-2976 (2003)

  		42. H. H. Gan and T. Schlick, "Methods for Macromolecular Modeling (M3): Assessment of Progress and Future Perspectives", in Computational Methods for Macromolecules: Challenges and Applications - Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modelling, New York, October 12-14, 2000, T. Schlick and H. H. Gan, eds., Lecture Notes in Computational Science and Engineering, Vol. 24, pp. 1-25, Springer Verlag, Berlin (2002)

  		43. J. Huang, Q. Zhang, and T. Schlick, "Effect of DNA Superhelicity and Bound Proteins on Mechanistic Aspects of the Hin-mediated and Fis-enhanced Inversion", Biophys. J., 85:804-817 (2003)

  		44. J. Aishima, R. K. Gitti, J. E. Noah, H. H. Gan, T. Schlick, and C. Wolberger, "A Hoogsteen Base Pair Embedded in Undistorted B-DNA", Nuc. Acids Res., 30:5244-5252 (2002)

  		45. H. H. Gan, S. Pasquali, and T. Schlick, "Exploring The Repertoire of RNA Secondary Motifs Using Graph Theory with Implications for RNA Design", Nuc. Acids Res., 31:2926-2943 (2003)

  		46. D. Xie and T. Schlick, "A More Lenient Stopping Rule for Line Search Algorithms", Optim. Meth. Softw., 17:683-700 (2002)

  		47. D. Xie, S. B. Singh, E. M. Fluder, and T. Schlick, "Principal Component Analysis Combined with Truncated-Newton Minimization for Dimensionality Reduction of Chemical Databases", Math. Program. Ser. B, 95:161-185 (2003)

  		48. J. Huang and T. Schlick, "Macroscopic Modeling and Simulations of Supercoiled DNA with Bound Proteins", J. Chem. Phys., 117:8573-8586 (2002)

  		49. D. Barash, T. Schlick, M. Israeli, and R. Kimmel, "Multiplicative Operator Splittings in Nonlinear Diffusion: From Spatial Splitting to Multiple Timesteps", J. Math. Imag. Vision, 19:33-48 (2003)

  		50. D. Strahs, D. Barash, X. Qian, and T. Schlick, "Sequence-Dependent Solution Structure and Motions of 13 TATA/TBP Complexes", Biopolymers, 69:216-243 (2003)

  		51. D. Barash, L. Yang, X. Qian, and T. Schlick, "Inherent Speedup Limitations in Multiple Timestep/ Particle Mesh Ewald Algorithms", J. Comp. Chem., 24:77-88 (2003)

  		52. L. Yang, W. A. Beard, S. H. Wilson, B. Roux, S. Broyde, and T. Schlick, "Local Deformations Revealed by Dynamics Simulations of DNA Polymerase with DNA Mismatches at the Primer Terminus", J. Mol. Biol., 321:459-478 (2002)

  		53. X. Qian and T. Schlick, "Efficient Multiple Timestep Integrators with Distance-Based Force Splitting for Particle-Mesh-Ewald Molecular Dynamics Simulations", J. Chem. Phys., 116:5971-5983 (2002)

  		54. P. F. Batcho and T. Schlick, "New Splitting Formulations for Lattice Summations", J. Chem. Phys., 115:8312-8326 (2001)

  		55. L. Yang, W. A. Beard, S. H. Wilson, S. Broyde, and T. Schlick, "Polymerase Simulations Reveal That Arg258 Rotation is a Slow Step Rather Than Large Subdomain Motions Per Se", J. Mol. Biol., 317:651-671 (2002)

  		56. T. Schlick, "Time-Trimming Tricks for Dynamic Simulations: Splitting Force Updates to Reduce Computational Work", Structure, 9:R45-R53 (2001)

  		57. P. F. Batcho and T. Schlick, "Special Stability Advantages of Position Verlet Over Velocity Verlet in Multiple-Timestep Integration", J. Chem. Phys., 115:4019-4029 (2001)

  		58. P. F. 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)

  		59. X. Qian, D. Strahs, and T. Schlick, "A New Program for Optimizing Periodic Boundary Models of Solvated Biomolecules (PBCAID)", J. Comp. Chem., 22:1843-1850 (2001)

  		60. H. H. Gan, R. A. Perlow, S. Roy, J. Ko, M. Wu, J. Huang, S. Yan, A. Nicoletta, J. Vafai, D. Sun, L. Wang, J. E. Noah, S. Pasquali, and T. Schlick, "Analysis of Protein Sequence/Structure Similarity Relationships", Biophys. J., 83:2781-2791 (2002)

  		61. X. Qian, D. Strahs, and T. Schlick, "Dynamic Simulations of 13 TATA Variants Refine Kinetic Hypotheses on Sequence/Activity Relationships", J. Mol. Biol., 308:681-703 (2001)

  		62. H. H. Gan, A. Tropsha, and T. Schlick, "Lattice Protein Folding with Two and Four-Body Statistical Potentials", Proteins: Struc. Func. Gen., 43: 161-174 (2001)

  		63. T. Schlick and L. Yang, "Long-Timestep Biomolecular Dynamics Simulations: LN Performance on a Polymerase Beta / DNA System", in Multiscale Computational Methods in Chemistry and Physics, Vol 177, NATO Science Series: Series III Computer and Systems Sciences, A. Brandt, J. Bernholc and K. Binder, eds., IOS Press, Amsterdam (2001)

  		64. D. A. Beard and T. Schlick, "Computational Modeling Predicts the Structure and Dynamics of Chromatin Fiber", Structure, 9:105-114, February (2001)

  		65. H. H. Gan, A. Tropsha, and T. Schlick, "Generating Folded Protein Structures with a Lattice Chain Growth Algorithm", J. Chem. Phys., 113:5511-5524, October (2000)

  		66. J. Huang, T. Schlick, and A. Vologodskii, "Dynamics of Site Juxtaposition in Supercoiled DNA", Proc. Natl. Acad. Sci., 98:968-973, January (2001)

  		67. T. Schlick, D. A. Beard, J. Huang, D. Strahs, and X. Qian, "Computational Challenges in Simulating Large DNA over Long Times", IEEE Computing in Science & Engineering, 2:38-51, Nov/Dec (2000)

  		68. D. A. Beard and T. Schlick, "Modeling Salt-Mediated Electrostatics of Macromolecules: The Discrete Surface Charge Optimization Algorithm and Its Application to the Nucleosome", Biopolymers, 58:106-115 , January (2001)

  		69. D. Strahs and T. Schlick, "A-tract Bending: Insights into Experimental Structures by Computational Models", J. Mol. Biol., 301:643-663, August (2000)

  		70. D. A. Beard and T. Schlick, "Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics", J. Chem. Phys., 112:7313-7322, May (2000)

  		71. D. A. Beard and T. Schlick, "Inertial Stochastic Dynamics. II. Influence of Inertia on Slow Kinetic Processes of Supercoiled DNA", J. Chem. Phys., 112:7323-7338, May (2000)

  		72. D. Xie and T. Schlick, "Visualization of Chemical Databases Using the Singular Value Decomposition and Truncated-Newton Minimization", Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches, Volume 40, pages 267-286, C. A. Floudas and P. M. Pardalos, eds., Kluwer Academic Publishers, Dororecht/Boston/London (2000)

  		73. T. Schlick, "Computational Molecular Biophysics Today: A Confluence of Methological Advances and Complex Biomolecular Applications", J. Comp. Phys., 151:1-8, May (1999)

  		74. A. Sandu and T. Schlick, "Resonance Analysis in Force Splitting Methods for Biomolecular Dynamics", J. Comp. Phys., 151:74-113, May (1999)

  		75. T. Schlick, R. D. Skeel, A. T. Brunger, L. V. Kalé, J. Hermans, K. Schulten, and J. A. Board, Jr., "Algorithmic Challenges in Computational Molecular Biophysics", J. Comp. Phys., 151:9-48, May (1999)

  		76. D. Xie and T. Schlick, "Efficient Implementation of the Truncated Newton Method for Large Scale Chemistry Applications", SIAM J. Opt., 10: 132-154 October (1999)

  		77. D. Xie and T. Schlick, "Remark on the Updated Truncated Newton Minimization Package, Algorithm 702", ACM Trans. Math. Softw., 25, 108-122, March (1999)

  		78. D. Xie, L. R. Scott and T. Schlick, "Analysis of the SHAKE-SOR Algorithm for Constrained Molecular Dynamics Simulations", Methods and Applications of Analysis, a Special issue dedicated to Prof. Cathleen Morawetz of the Courant Institute, 7: 577-590, September (2000)

  		79. D. Xie, A. Tropsha and T. Schlick, "An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization", J. Chem. Inf. Comput. Sci., 40:167-177, December (1999)

  		80. E. Barth and T. Schlick, "I. Overcoming Stability Limitations in Biomolecular Dynamics: Combining Force Splitting via Extrapolation with Langevin Dynamics in LN", J. Chem. Phys., 109:1617-1632, August (1998)

  		81. E. Barth and T. Schlick, "II. Extrapolation Versus Impulse in Multiple-Timestepping Schemes: Linear Analysis and Applications to Newtonian and Langevin Dynamics", J. Chem. Phys. 109:1633-1642, August (1998)

  		82. P. Derreumaux and T. Schlick, "Simulation of the Loop Opening/Closing of the Enzyme Triosephosphate Isomeraze (TIM)", Biophys. J., 74:72-81, January (1998)

  		83. H. Jian, T. Schlick, and A. Vologodskii, "Internal Motion of Supercoiled DNA: Brownian Dynamics Simulations of Site Juxtaposition", J. Mol. Biol., 284:287-296, November (1998)

  		84. T. Schlick, "Geometry Optimization", Contributed chapter to the Encyclopedia of Computational Chemistry (5 Volumes), Volume 2, pages 1136-1157, P. von Rague Schleyer, Editor in Chief and N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, and H. F. Schaefer III, eds., John Wiley & Sons, West Sussex (1998)

  		85. T. Schlick, "Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations", in Algorithms for Macromolecular Modeling, Volume 4, pages 227-262, Springer-Verlag series in "Lecture Notes in Computational Science and Engineering", P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, R. D. Skeel, and S. Reich, eds. (1998)

  		86. T. Schlick, M. Mandziuk, R. D. Skeel, and K. Srinivas, "Nonlinear Resonance Artifacts in Molecular Dynamics", J. Comp. Phys., 139:1-29, February (1998)

  		87. L. Y. Zaslavsky and T. Schlick, "An Adaptive Multigrid Technique for Evaluating Long-Range Forces in Biomolecular Simulations", App. Math. Comp., 97:237-250, December (1998)

  		88. E. Barth, M. Mandziuk, and T. Schlick, "A Separating Framework for Increasing the Timestep in Molecular Dynamics", contributed chapter to Computer Simulation of Biomolecular Systems, Volume 3, Chapter 4, pages 97-120, W. van Gunsteren, P. Weiner and T. Wilkinson eds., ESCOM Science Publishers, Ledien, The Netherlands (1997)

  		89. H. Jian, A. Vologodskii, and T. Schlick, "A Combined Wormlike Chain and Bead Model for Dynamic Simulations of Long DNA", J. Comp. Phys., 136:168-179, September (1997)

  		90. G. Liu, T. Schlick, A. J. Olson, and W. K. Olson, "Configurational Transitions in DNA Supercoils Represented by Fourier-Series Curve-Fitting Techniques", Biophys. J., 73:1742-1762, October (1997)

  		91. G. Ramachandran and T. Schlick, "On Buckling Transitions in Supercoiled DNA: Dependence on Elastic Constants and DNA Size", Biopolymers, 41:5-25, January (1997)

  		92. T. Schlick, E. Barth, and M. Mandziuk, "Biomolecular Dynamics at Long Timesteps: Bridging the Time Scale Gap Between Simulation and Experimentation", Annu. Rev. Biophys. Biomol. Struct., 26:181-222 (1997)

  		93. R. D. Skeel, G. Zhang and T. Schlick, "A Family of Symplectic Integrators: Stability, Accuracy, and Molecular Dynamics Applications", SIAM J. Sci. Comp., 18:203-222 (1997)

  		94. B. Mishra and T. Schlick, " The Notion of Error in Langevin Dynamics: (1) Linear Analysis", J. Chem. Phys., 105:299-318, July (1996)

  		95. T. Pinou, T. Schlick, B. Li, and H. Dowling, "Addition of Darwin's Third Dimension to Evolutionary Trees", J. Theor. Bio., 219:505-512, October (1996)

  		96. G. Ramachandran and T. Schlick, "Beyond Optimization: Simulating the Dynamics of Supercoiled DNA by a Macroscopic Model", in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Volume 23, Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, P. Pardalos, D. Shalloway, and G. Xue, eds., pages