Tamar Schlick - Publications

Program in Computational Biology New York University, New York, NY, United States 
Bioinformatics, Biochemistry

164 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Sridhar A, Farr SE, Portella G, Schlick T, Orozco M, Collepardo-Guevara R. Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry. Proceedings of the National Academy of Sciences of the United States of America. PMID 32165536 DOI: 10.1073/Pnas.1910044117  0.669
2020 Jain S, Zhu Q, Paz ASP, Schlick T. Identification of novel RNA design candidates by clustering the extended RNA-as-graphs library. Biochimica Et Biophysica Acta. General Subjects. 129534. PMID 31954797 DOI: 10.1016/J.Bbagen.2020.129534  0.378
2019 Jain S, Tao Y, Schlick T. Inverse Folding with RNA-As-Graphs Produces a Large Pool of Candidate Sequences with Target Topologies. Journal of Structural Biology. 107438. PMID 31874236 DOI: 10.1016/J.Jsb.2019.107438  0.393
2019 Myers CG, Olins DE, Olins AL, Schlick T. Mesoscale Modeling of Nucleosome-Binding Antibody PL2-6: Mono- versus Bivalent Chromatin Complexes. Biophysical Journal. PMID 31668748 DOI: 10.1016/J.Bpj.2019.08.019  0.311
2019 Meng G, Tariq M, Jain S, Elmetwaly S, Schlick T. RAG-Web: RNA Structure Prediction/Design using RNA-As-Graphs. Bioinformatics (Oxford, England). PMID 31373604 DOI: 10.1093/Bioinformatics/Btz611  0.399
2019 Jung J, Nishima W, Daniels M, Bascom G, Kobayashi C, Adedoyin A, Wall M, Lappala A, Phillips D, Fischer W, Tung CS, Schlick T, Sugita Y, Sanbonmatsu KY. Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations. Journal of Computational Chemistry. PMID 30994934 DOI: 10.1002/Jcc.25840  0.312
2019 Perišić O, Portillo-Ledesma S, Schlick T. Sensitive effect of linker histone binding mode and subtype on chromatin condensation. Nucleic Acids Research. PMID 30968131 DOI: 10.1093/Nar/Gkz234  0.342
2019 Jain S, Saju S, Petingi L, Schlick T. An Extended Dual Graph Library and Partitioning Algorithm Applicable to Pseudoknotted RNA Structures. Methods (San Diego, Calif.). PMID 30928508 DOI: 10.1016/J.Ymeth.2019.03.022  0.354
2019 Bascom GD, Myers CG, Schlick T. Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub. Proceedings of the National Academy of Sciences of the United States of America. PMID 30718394 DOI: 10.1073/Pnas.1816424116  0.322
2019 Sridhar A, Farr S, Portella G, Schlick T, Orozco M, Collepardo-Guevara R. Chromatin Structure Regulation by an Epigenetic Switch Tuning the Flexibility of the H1 C-Terminal Domain Biophysical Journal. 116: 70a. DOI: 10.1016/J.Bpj.2018.11.420  0.644
2018 Jain S, Laederach A, V Ramos SB, Schlick T. A pipeline for computational design of novel RNA-like topologies. Nucleic Acids Research. 46: 7040-7051. PMID 30137633 DOI: 10.1093/Nar/Gky524  0.399
2018 Jain S, Bayrak CS, Petingi L, Schlick T. Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs. Genes. 9. PMID 30044451 DOI: 10.3390/Genes9080371  0.394
2018 Bascom GD, Schlick T. Chromatin Fiber Folding Directed by Cooperative Histone Tail Acetylation and Linker Histone Binding. Biophysical Journal. PMID 29655483 DOI: 10.1016/J.Bpj.2018.03.008  0.312
2018 Schlick T. Adventures with RNA Graphs. Methods (San Diego, Calif.). PMID 29621619 DOI: 10.1016/J.Ymeth.2018.03.009  0.422
2017 Jain S, Schlick T. F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly. Journal of Molecular Biology. PMID 28988954 DOI: 10.1016/J.Jmb.2017.09.017  0.405
2017 Perišić O, Schlick T. Dependence of the Linker Histone and Chromatin Condensation on the Nucleosome Environment. The Journal of Physical Chemistry. B. PMID 28732449 DOI: 10.1021/Acs.Jpcb.7B04917  0.383
2017 Schlick T, Pyle A. RNA Structural Variability and Functional Versatility Challenges RNA Structural Modeling and Design. Biophysical Journal. PMID 28669406 DOI: 10.1016/J.Bpj.2017.06.040  0.429
2017 Bascom GD, Kim T, Schlick T. Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome Depletion. The Journal of Physical Chemistry. B. PMID 28299939 DOI: 10.1021/Acs.Jpcb.7B00998  0.325
2017 Schlick T, Pyle AM. Opportunities and Challenges in RNA Structural Modeling and Design. Biophysical Journal. PMID 28162235 DOI: 10.1016/J.Bpj.2016.12.037  0.415
2017 Bayrak CS, Kim N, Schlick T. Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction. Nucleic Acids Research. PMID 28158755 DOI: 10.1093/Nar/Gkx045  0.596
2017 Bascom G, Schlick T. Linking Chromatin Fibers to Gene Folding by Hierarchical Looping. Biophysical Journal. PMID 28153411 DOI: 10.1016/J.Bpj.2017.01.003  0.364
2017 Schlick T, Loew L. Unraveling Genome Biophysics. Biophysical Journal. PMID 28109530 DOI: 10.1016/J.Bpj.2017.01.002  0.358
2016 Perišić O, Schlick T. Computational strategies to address chromatin structure problems. Physical Biology. 13: 035006. PMID 27345617 DOI: 10.1088/1478-3975/13/3/035006  0.367
2016 Luque A, Ozer G, Schlick T. Correlation among DNA Linker Length, Linker Histone Concentration, and Histone Tails in Chromatin. Biophysical Journal. 110: 2309-19. PMID 27276249 DOI: 10.1016/J.Bpj.2016.04.024  0.349
2016 Bascom GD, Sanbonmatsu KY, Schlick T. Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements. The Journal of Physical Chemistry. B. PMID 27218881 DOI: 10.1021/Acs.Jpcb.6B03197  0.369
2016 Kim T, Freudenthal BD, Beard WA, Wilson SH, Schlick T. Insertion of oxidized nucleotide triggers rapid DNA polymerase opening. Nucleic Acids Research. PMID 27034465 DOI: 10.1093/Nar/Gkw174  0.34
2016 Pyle AM, Schlick T. Challenges in RNA Structural Modeling and Design. Journal of Molecular Biology. PMID 26876599 DOI: 10.1016/J.Jmb.2016.02.012  0.368
2016 Hua L, Song Y, Kim N, Laing C, Wang JT, Schlick T. CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking. Plos One. 11: e0147097. PMID 26789998 DOI: 10.1371/Journal.Pone.0147097  0.607
2016 Grigoryev SA, Bascom G, Buckwalter JM, Schubert MB, Woodcock CL, Schlick T. Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes. Proceedings of the National Academy of Sciences of the United States of America. PMID 26787893 DOI: 10.1073/Pnas.1518280113  0.328
2015 Baba N, Elmetwaly S, Kim N, Schlick T. Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach. Journal of Molecular Biology. PMID 26478223 DOI: 10.1016/J.Jmb.2015.10.009  0.609
2015 Zahran M, Sevim Bayrak C, Elmetwaly S, Schlick T. RAG-3D: a search tool for RNA 3D substructures. Nucleic Acids Research. 43: 9474-88. PMID 26304547 DOI: 10.1093/Nar/Gkv823  0.378
2015 Collepardo-Guevara R, Portella G, Vendruscolo M, Frenkel D, Schlick T, Orozco M. Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study. Journal of the American Chemical Society. 137: 10205-15. PMID 26192632 DOI: 10.1021/Jacs.5B04086  0.721
2015 Ozer G, Luque A, Schlick T. The chromatin fiber: multiscale problems and approaches. Current Opinion in Structural Biology. 31: 124-39. PMID 26057099 DOI: 10.1016/J.Sbi.2015.04.002  0.353
2015 Kim N, Zahran M, Schlick T. Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP: a hierarchical graph sampling approach. Methods in Enzymology. 553: 115-35. PMID 25726463 DOI: 10.1016/Bs.Mie.2014.10.054  0.599
2015 Ozer G, Collepardo-Guevara R, Schlick T. Forced unraveling of chromatin fibers with nonuniform linker DNA lengths. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 27: 064113. PMID 25564319 DOI: 10.1088/0953-8984/27/6/064113  0.677
2015 Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH. Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature. 517: 635-9. PMID 25409153 DOI: 10.1038/Nature13886  0.353
2014 Kim N, Zheng Z, Elmetwaly S, Schlick T. RNA graph partitioning for the discovery of RNA modularity: a novel application of graph partition algorithm to biology. Plos One. 9: e106074. PMID 25188578 DOI: 10.1371/Journal.Pone.0106074  0.586
2014 Luque A, Collepardo-Guevara R, Grigoryev S, Schlick T. Dynamic condensation of linker histone C-terminal domain regulates chromatin structure. Nucleic Acids Research. 42: 7553-60. PMID 24906881 DOI: 10.1093/Nar/Gku491  0.691
2014 Collepardo-Guevara R, Schlick T. Chromatin fiber polymorphism triggered by variations of DNA linker lengths. Proceedings of the National Academy of Sciences of the United States of America. 111: 8061-6. PMID 24847063 DOI: 10.1073/Pnas.1315872111  0.676
2014 Kim N, Laing C, Elmetwaly S, Jung S, Curuksu J, Schlick T. Graph-based sampling for approximating global helical topologies of RNA. Proceedings of the National Academy of Sciences of the United States of America. 111: 4079-84. PMID 24591615 DOI: 10.1073/Pnas.1318893111  0.792
2014 Li Y, Freudenthal BD, Beard WA, Wilson SH, Schlick T. Optimal and variant metal-ion routes in DNA polymerase β's conformational pathways. Journal of the American Chemical Society. 136: 3630-9. PMID 24511902 DOI: 10.1021/Ja412701F  0.351
2014 Jung S, Schlick T. Interconversion between parallel and antiparallel conformations of a 4H RNA junction in domain 3 of foot-and-mouth disease virus IRES captured by dynamics simulations. Biophysical Journal. 106: 447-58. PMID 24461020 DOI: 10.1016/J.Bpj.2013.12.008  0.785
2013 Kim N, Petingi L, Schlick T. Network Theory Tools for RNA Modeling. Wseas Transactions On Mathematics. 9: 941-955. PMID 25414570  0.554
2013 Sampoli Benítez B, Barbati ZR, Arora K, Bogdanovic J, Schlick T. How DNA polymerase X preferentially accommodates incoming dATP opposite 8-oxoguanine on the template. Biophysical Journal. 105: 2559-68. PMID 24314086 DOI: 10.1016/J.Bpj.2013.10.014  0.673
2013 Laing C, Jung S, Kim N, Elmetwaly S, Zahran M, Schlick T. Predicting helical topologies in RNA junctions as tree graphs. Plos One. 8: e71947. PMID 23991010 DOI: 10.1371/Journal.Pone.0071947  0.805
2013 Li Y, Schlick T. "Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides. Plos Computational Biology. 9: e1003074. PMID 23717197 DOI: 10.1371/Journal.Pcbi.1003074  0.413
2013 Collepardo-Guevara R, Schlick T. Insights into chromatin fibre structure by in vitro and in silico single-molecule stretching experiments. Biochemical Society Transactions. 41: 494-500. PMID 23514142 DOI: 10.1042/Bst20120349  0.676
2013 Jung S, Schlick T. Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site. Nucleic Acids Research. 41: 1483-95. PMID 23275533 DOI: 10.1093/Nar/Gks1302  0.775
2012 Schlick T, Arora K, Beard WA, Wilson SH. Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms. Theoretical Chemistry Accounts. 131: 1287. PMID 23459563 DOI: 10.1007/S00214-012-1287-7  0.673
2012 Collepardo-Guevara R, Schlick T. Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes. Nucleic Acids Research. 40: 8803-17. PMID 22790986 DOI: 10.1093/Nar/Gks600  0.693
2012 Li Y, Gridley CL, Jaeger J, Sweasy JB, Schlick T. Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway. Journal of the American Chemical Society. 134: 9999-10010. PMID 22651551 DOI: 10.1021/Ja300361R  0.316
2012 Kim N, Schlick T. A new toolkit for modeling RNA from a pseudo-torsional space: commentary on "discrete RNA libraries from pseudo-torsional space" by Humphris-Narayanan and Pyle (J. Mol. Biol. March 2012). Journal of Molecular Biology. 421: 1-5. PMID 22634179 DOI: 10.1016/J.Jmb.2012.05.027  0.569
2012 Quarta G, Sin K, Schlick T. Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function. Plos Computational Biology. 8: e1002368. PMID 22359488 DOI: 10.1371/Journal.Pcbi.1002368  0.367
2012 Schlick T, Hayes J, Grigoryev S. Toward convergence of experimental studies and theoretical modeling of the chromatin fiber. The Journal of Biological Chemistry. 287: 5183-91. PMID 22157002 DOI: 10.1074/Jbc.R111.305763  0.342
2012 Laing C, Wen D, Wang JT, Schlick T. Predicting coaxial helical stacking in RNA junctions. Nucleic Acids Research. 40: 487-98. PMID 21917853 DOI: 10.1093/Nar/Gkr629  0.379
2012 Foley MC, Arora K, Schlick T. Chapter 4: Intrinsic motions of DNA polymerases underlie their remarkable specificity and selectivity and suggest a hybrid substrate binding mechanism Rsc Biomolecular Sciences. 81-110.  0.781
2011 Collepardo-Guevara R, Schlick T. The effect of linker histone's nucleosome binding affinity on chromatin unfolding mechanisms. Biophysical Journal. 101: 1670-80. PMID 21961593 DOI: 10.1016/J.Bpj.2011.07.044  0.689
2011 Izzo JA, Kim N, Elmetwaly S, Schlick T. RAG: an update to the RNA-As-Graphs resource. Bmc Bioinformatics. 12: 219. PMID 21627789 DOI: 10.1186/1471-2105-12-219  0.603
2011 Laing C, Schlick T. Computational approaches to RNA structure prediction, analysis, and design. Current Opinion in Structural Biology. 21: 306-18. PMID 21514143 DOI: 10.1016/J.Sbi.2011.03.015  0.421
2011 Schlick T, Collepardo-Guevara R, Halvorsen LA, Jung S, Xiao X. Biomolecularmodeling and simulation: a field coming of age. Quarterly Reviews of Biophysics. 44: 191-228. PMID 21226976 DOI: 10.1017/S0033583510000284  0.781
2010 Laing C, Schlick T. Computational approaches to 3D modeling of RNA. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 22: 283101. PMID 21399271 DOI: 10.1088/0953-8984/22/28/283101  0.416
2010 Li Y, Schlick T. Modeling DNA polymerase μ motions: subtle transitions before chemistry. Biophysical Journal. 99: 3463-72. PMID 21081096 DOI: 10.1016/J.Bpj.2010.09.056  0.428
2010 Gan HH, Schlick T. Chromatin ionic atmosphere analyzed by a mesoscale electrostatic approach. Biophysical Journal. 99: 2587-96. PMID 20959100 DOI: 10.1016/J.Bpj.2010.08.023  0.34
2010 Foley MC, Padow VA, Schlick T. DNA pol λ's extraordinary ability to stabilize misaligned DNA. Journal of the American Chemical Society. 132: 13403-16. PMID 20822183 DOI: 10.1021/Ja1049687  0.782
2010 Perišić O, Collepardo-Guevara R, Schlick T. Modeling studies of chromatin fiber structure as a function of DNA linker length. Journal of Molecular Biology. 403: 777-802. PMID 20709077 DOI: 10.1016/J.Jmb.2010.07.057  0.674
2010 Kim N, Izzo JA, Elmetwaly S, Gan HH, Schlick T. Computational generation and screening of RNA motifs in large nucleotide sequence pools. Nucleic Acids Research. 38: e139. PMID 20448026 DOI: 10.1093/Nar/Gkq282  0.599
2010 Schlick T. Mathematical and Biological Scientists Assess the State-of-the-Art in RNA Science at an IMA Workshop RNA in Biology, Bioengineering and Biotechnology International Journal For Multiscale Computational Engineering. 8: 369-378. DOI: 10.1615/Intjmultcompeng.V8.I4.20  0.391
2009 Schlick T. Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure. F1000 Biology Reports. 1: 48. PMID 20948637 DOI: 10.3410/B1-48  0.328
2009 Schlick T. Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules. F1000 Biology Reports. 1: 51. PMID 20948633 DOI: 10.3410/B1-51  0.329
2009 Schlick T, Perisić O. Mesoscale simulations of two nucleosome-repeat length oligonucleosomes. Physical Chemistry Chemical Physics : Pccp. 11: 10729-37. PMID 20145817 DOI: 10.1039/B918629H  0.307
2009 Quarta G, Kim N, Izzo JA, Schlick T. Analysis of riboswitch structure and function by an energy landscape framework. Journal of Molecular Biology. 393: 993-1003. PMID 19733179 DOI: 10.1016/J.Jmb.2009.08.062  0.597
2009 Laing C, Jung S, Iqbal A, Schlick T. Tertiary motifs revealed in analyses of higher-order RNA junctions. Journal of Molecular Biology. 393: 67-82. PMID 19660472 DOI: 10.1016/J.Jmb.2009.07.089  0.779
2009 Grigoryev SA, Arya G, Correll S, Woodcock CL, Schlick T. Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions. Proceedings of the National Academy of Sciences of the United States of America. 106: 13317-22. PMID 19651606 DOI: 10.1073/Pnas.0903280106  0.366
2009 Foley MC, Schlick T. Relationship between conformational changes in pol lambda's active site upon binding incorrect nucleotides and mismatch incorporation rates. The Journal of Physical Chemistry. B. 113: 13035-47. PMID 19572669 DOI: 10.1021/Jp903172X  0.781
2009 Laing C, Schlick T. Analysis of four-way junctions in RNA structures. Journal of Molecular Biology. 390: 547-59. PMID 19445952 DOI: 10.1016/J.Jmb.2009.04.084  0.425
2009 Arya G, Schlick T. A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments. The Journal of Physical Chemistry. A. 113: 4045-59. PMID 19298048 DOI: 10.1021/Jp810375D  0.346
2008 Xin Y, Quarta G, Gan HH, Schlick T. Estimating the fraction of non-coding RNAs in mammalian transcriptomes. Bioinformatics and Biology Insights. 2: 75-94. PMID 19812767 DOI: 10.4137/Bbi.S443  0.385
2008 Xin Y, Laing C, Leontis NB, Schlick T. Annotation of tertiary interactions in RNA structures reveals variations and correlations. Rna (New York, N.Y.). 14: 2465-77. PMID 18957492 DOI: 10.1261/Rna.1249208  0.409
2008 Sampoli Benítez BA, Arora K, Balistreri L, Schlick T. Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation. Journal of Molecular Biology. 384: 1086-97. PMID 18955064 DOI: 10.1016/J.Jmb.2008.10.025  0.638
2008 Wang Y, Schlick T. Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization. Journal of the American Chemical Society. 130: 13240-50. PMID 18785738 DOI: 10.1021/Ja802215C  0.336
2008 Sridhar P, Gan HH, Schlick T. A computational screen for C/D box snoRNAs in the human genomic region associated with Prader-Willi and Angelman syndromes. Journal of Biomedical Science. 15: 697-705. PMID 18661287 DOI: 10.1007/S11373-008-9271-X  0.352
2008 Bebenek K, Garcia-Diaz M, Foley MC, Pedersen LC, Schlick T, Kunkel TA. Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda. Embo Reports. 9: 459-64. PMID 18369368 DOI: 10.1038/Embor.2008.33  0.785
2008 Foley MC, Schlick T. Simulations of DNA pol lambda R517 mutants indicate 517's crucial role in ternary complex stability and suggest DNA slippage origin. Journal of the American Chemical Society. 130: 3967-77. PMID 18307346 DOI: 10.1021/Ja077982T  0.787
2007 Kim N, Shin JS, Elmetwaly S, Gan HH, Schlick T. RagPools: RNA-As-Graph-Pools--a web server for assisting the design of structured RNA pools for in vitro selection. Bioinformatics (Oxford, England). 23: 2959-60. PMID 17855416 DOI: 10.1093/Bioinformatics/Btm439  0.601
2007 Bojin MD, Schlick T. A quantum mechanical investigation of possible mechanisms for the nucleotidyl transfer reaction catalyzed by DNA polymerase beta. The Journal of Physical Chemistry. B. 111: 11244-52. PMID 17764165 DOI: 10.1021/Jp071838C  0.779
2007 Alberts IL, Wang Y, Schlick T. DNA polymerase beta catalysis: are different mechanisms possible? Journal of the American Chemical Society. 129: 11100-10. PMID 17696533 DOI: 10.1021/Ja071533B  0.401
2007 Kim N, Gan HH, Schlick T. A computational proposal for designing structured RNA pools for in vitro selection of RNAs. Rna (New York, N.Y.). 13: 478-92. PMID 17322501 DOI: 10.1261/Rna.374907  0.602
2007 Wang Y, Schlick T. Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides. Bmc Structural Biology. 7: 7. PMID 17313689 DOI: 10.1186/1472-6807-7-7  0.351
2007 Wang Y, Reddy S, Beard WA, Wilson SH, Schlick T. Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta. Biophysical Journal. 92: 3063-70. PMID 17293403 DOI: 10.1529/Biophysj.106.092106  0.343
2006 Radhakrishnan R, Arora K, Wang Y, Beard WA, Wilson SH, Schlick T. Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection. Biochemistry. 45: 15142-56. PMID 17176036 DOI: 10.1021/Bi061353Z  0.69
2006 Arya G, Schlick T. Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model. Proceedings of the National Academy of Sciences of the United States of America. 103: 16236-41. PMID 17060627 DOI: 10.1073/Pnas.0604817103  0.352
2006 Radhakrishnan R, Schlick T. Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta. Biochemical and Biophysical Research Communications. 350: 521-9. PMID 17022941 DOI: 10.1016/J.Bbrc.2006.09.059  0.41
2006 Foley MC, Arora K, Schlick T. Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda. Biophysical Journal. 91: 3182-95. PMID 16920835 DOI: 10.1529/Biophysj.106.092080  0.79
2006 Arya G, Zhang Q, Schlick T. Flexible histone tails in a new mesoscopic oligonucleosome model. Biophysical Journal. 91: 133-50. PMID 16603492 DOI: 10.1529/Biophysj.106.083006  0.337
2006 Zhang Q, Schlick T. Stereochemistry and position-dependent effects of carcinogens on TATA/TBP binding. Biophysical Journal. 90: 1865-77. PMID 16387764 DOI: 10.1529/Biophysj.105.074344  0.401
2006 Wang Y, Arora K, Schlick T. Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass. Protein Science : a Publication of the Protein Society. 15: 135-51. PMID 16322565 DOI: 10.1110/Ps.051726906  0.674
2006 Sampoli Benítez BA, Arora K, Schlick T. In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanism. Biophysical Journal. 90: 42-56. PMID 16214865 DOI: 10.1529/Biophysj.105.071944  0.659
2006 Laserson U, Gan HH, Schlick T. Exploring the Connection Between Synthetic and Natural RNAs in Genomes: A Novel Computational Approach Lecture Notes in Computational Science and Engineering. 49: 35-56.  0.739
2005 Arora K, Schlick T. Conformational transition pathway of polymerase beta/DNA upon binding correct incoming substrate. The Journal of Physical Chemistry. B. 109: 5358-67. PMID 16863202 DOI: 10.1021/Jp0446377  0.668
2005 Laserson U, Gan HH, Schlick T. Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs. Nucleic Acids Research. 33: 6057-69. PMID 16254081 DOI: 10.1093/Nar/Gki911  0.741
2005 Arora K, Beard WA, Wilson SH, Schlick T. Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity. Biochemistry. 44: 13328-41. PMID 16201758 DOI: 10.1021/Bi0507682  0.672
2005 Radhakrishnan R, Schlick T. Fidelity discrimination in DNA polymerase beta: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair. Journal of the American Chemical Society. 127: 13245-52. PMID 16173754 DOI: 10.1021/Ja052623O  0.417
2005 Gevertz J, Gan HH, Schlick T. In vitro RNA random pools are not structurally diverse: a computational analysis. Rna (New York, N.Y.). 11: 853-63. PMID 15923372 DOI: 10.1261/Rna.7271405  0.419
2005 Sun J, Zhang Q, Schlick T. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation. Proceedings of the National Academy of Sciences of the United States of America. 102: 8180-5. PMID 15919827 DOI: 10.1073/Pnas.0408867102  0.391
2005 Pasquali S, Gan HH, Schlick T. Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs. Nucleic Acids Research. 33: 1384-98. PMID 15745998 DOI: 10.1093/Nar/Gki267  0.425
2004 Arora K, Schlick T. In silico evidence for DNA polymerase-beta's substrate-induced conformational change. Biophysical Journal. 87: 3088-99. PMID 15507687 DOI: 10.1529/Biophysj.104.040915  0.682
2004 Kim N, Shiffeldrim N, Gan HH, Schlick T. Candidates for novel RNA topologies. Journal of Molecular Biology. 341: 1129-44. PMID 15321711 DOI: 10.1016/J.Jmb.2004.06.054  0.61
2004 Zhang Q, Broyde S, Schlick T. Deformations of promoter DNA bound to carcinogens help interpret effects on TATA-element structure and activity. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 362: 1479-96. PMID 15306462 DOI: 10.1098/Rsta.2004.1386  0.425
2004 Fera D, Kim N, Shiffeldrim N, Zorn J, Laserson U, Gan HH, Schlick T. RAG: RNA-As-Graphs web resource. Bmc Bioinformatics. 5: 88. PMID 15238163 DOI: 10.1186/1471-2105-5-88  0.781
2004 Yang L, Arora K, Beard WA, Wilson SH, Schlick T. Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly. Journal of the American Chemical Society. 126: 8441-53. PMID 15238001 DOI: 10.1021/Ja049412O  0.641
2004 Yang L, Beard WA, Wilson SH, Broyde S, Schlick T. Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses. Biophysical Journal. 86: 3392-408. PMID 15189842 DOI: 10.1529/Biophysj.103.036012  0.372
2004 Radhakrishnan R, Schlick T. Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing. Proceedings of the National Academy of Sciences of the United States of America. 101: 5970-5. PMID 15069184 DOI: 10.1073/Pnas.0308585101  0.396
2004 Gan HH, Fera D, Zorn J, Shiffeldrim N, Tang M, Laserson U, Kim N, Schlick T. RAG: RNA-As-Graphs database--concepts, analysis, and features. Bioinformatics (Oxford, England). 20: 1285-91. PMID 14962931 DOI: 10.1093/Bioinformatics/Bth084  0.781
2004 Zorn J, Gan HH, Shiffeldrim N, Schlick T. Structural motifs in ribosomal RNAs: implications for RNA design and genomics. Biopolymers. 73: 340-7. PMID 14755570 DOI: 10.1002/Bip.10525  0.419
2004 Laserson U, Gan HH, Schlick T. Searching for 2D RNA geometries in bacterial genomes Proceedings of the Annual Symposium On Computational Geometry. 373-377.  0.714
2003 Zhang Q, Beard DA, Schlick T. Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm. Journal of Computational Chemistry. 24: 2063-74. PMID 14531059 DOI: 10.1002/Jcc.10337  0.304
2003 Huang J, Zhang Q, Schlick T. Effect of DNA superhelicity and bound proteins on mechanistic aspects of the Hin-mediated and Fis-enhanced inversion. Biophysical Journal. 85: 804-17. PMID 12885629 DOI: 10.1016/S0006-3495(03)74521-4  0.398
2003 Gan HH, Pasquali S, Schlick T. Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Research. 31: 2926-43. PMID 12771219 DOI: 10.1093/Nar/Gkg365  0.403
2003 Strahs D, Barash D, Qian X, Schlick T. Sequence-dependent solution structure and motions of 13 TATA/TBP (TATA-box binding protein) complexes. Biopolymers. 69: 216-43. PMID 12767124 DOI: 10.1002/Bip.10409  0.599
2003 Barash D, Yang L, Qian X, Schlick T. Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms. Journal of Computational Chemistry. 24: 77-88. PMID 12483677 DOI: 10.1002/Jcc.10196  0.57
2003 Arora K, Schlick T. Deoxyadenosine sugar puckering pathway simulated by the stochastic difference equation algorithm Chemical Physics Letters. 378: 1-8. DOI: 10.1016/S0009-2614(03)01195-3  0.595
2002 Aishima J, Gitti RK, Noah JE, Gan HH, Schlick T, Wolberger C. A Hoogsteen base pair embedded in undistorted B-DNA. Nucleic Acids Research. 30: 5244-52. PMID 12466549 DOI: 10.1093/Nar/Gkf661  0.405
2002 Yang L, Beard W, Wilson S, Roux B, Broyde S, Schlick T. Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus. Journal of Molecular Biology. 321: 459-78. PMID 12162959 DOI: 10.1016/S0022-2836(02)00617-4  0.425
2002 Yang L, Beard WA, Wilson SH, Broyde S, Schlick T. Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. Journal of Molecular Biology. 317: 651-71. PMID 11955015 DOI: 10.1006/Jmbi.2002.5450  0.412
2002 Huang J, Schlick T. Macroscopic modeling and simulations of supercoiled DNA with bound proteins Journal of Chemical Physics. 117: 8573-8586. DOI: 10.1063/1.1511506  0.378
2002 Qian X, Schlick T. Letters to the editor Journal of Chemical Physics. 117: 1927. DOI: 10.1063/1.1487820  0.406
2002 Qian X, Schlick T. Efficient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations Journal of Chemical Physics. 116: 5971-5983. DOI: 10.1063/1.1458542  0.546
2001 Qian X, Strahs D, Schlick T. A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID). Journal of Computational Chemistry. 22: 1843-1850. PMID 12116415 DOI: 10.1002/Jcc.1135  0.52
2001 Qian X, Strahs D, Schlick T. Dynamic simulations of 13 TATA variants refine kinetic hypotheses of sequence/activity relationships. Journal of Molecular Biology. 308: 681-703. PMID 11350169 DOI: 10.1006/Jmbi.2001.4617  0.625
2001 Beard DA, Schlick T. Computational modeling predicts the structure and dynamics of chromatin fiber. Structure (London, England : 1993). 9: 105-14. PMID 11250195 DOI: 10.1016/S0969-2126(01)00572-X  0.361
2001 Huang J, Schlick T, Vologodskii A. Dynamics of site juxtaposition in supercoiled DNA Proceedings of the National Academy of Sciences of the United States of America. 98: 968-973. PMID 11158579 DOI: 10.1073/Pnas.98.3.968  0.371
2001 Beard DA, Schlick T. Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome. Biopolymers. 58: 106-15. PMID 11072233 DOI: 10.1002/1097-0282(200101)58:1<106::Aid-Bip100>3.0.Co;2-#  0.301
2000 Strahs D, Schlick T. A-Tract bending: Insights into experimental structures by computational models Journal of Molecular Biology. 301: 643-663. PMID 10966775 DOI: 10.1006/Jmbi.2000.3863  0.401
2000 Beard DA, Schlick T. Inertial stochastic dynamics. II. Influence of inertia on slow kinetic processes of supercoiled DNA The Journal of Chemical Physics. 112: 7323-7338. DOI: 10.1063/1.481371  0.361
2000 Beard DA, Schlick T. Inertial stochastic dynamics. I. Long-time-step methods for Langevin dynamics The Journal of Chemical Physics. 112: 7313-7322. DOI: 10.1063/1.481331  0.308
2000 Schlick T, Beard DA, Huang J, Strahs DA, Qian X. Computational challenges in simulating large DNA over long times Computing in Science and Engineering. 2: 38-51.  0.552
1999 Xie D, Schlick T. Efficient implementation of the truncated-newton algorithm for large-scale chemistry applications Siam Journal On Optimization. 10: 132-154. DOI: 10.1137/S1052623497313642  0.306
1999 Sandu A, Schlick T. Masking Resonance Artifacts in Force-Splitting Methods for Biomolecular Simulations by Extrapolative Langevin Dynamics Journal of Computational Physics. 151: 74-113. DOI: 10.1006/Jcph.1999.6202  0.319
1998 Jian H, Schlick T, Vologodskii A. Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition Journal of Molecular Biology. 284: 287-296. PMID 9813118 DOI: 10.1006/Jmbi.1998.2170  0.407
1998 Derreumaux P, Schlick T. The loop opening/closing motion of the enzyme triosephosphate isomerase Biophysical Journal. 74: 72-81. PMID 9449311 DOI: 10.1016/S0006-3495(98)77768-9  0.331
1998 Barth E, Schlick T. Extrapolation versus impulse in multiple-timestepping schemes. II. Linear analysis and applications to Newtonian and Langevin dynamics Journal of Chemical Physics. 109: 1633-1642. DOI: 10.1063/1.476737  0.305
1997 Liu G, Schlick T, Olson AJ, Olson WK. Configurational transitions in Fourier series-represented DNA supercoils. Biophysical Journal. 73: 1742-62. PMID 9336170 DOI: 10.1016/S0006-3495(97)78205-5  0.361
1997 Schlick T, Barth E, Mandziuk M. Biomolecular dynamics at long timesteps: Bridging the timescale gap between simulation and experimentation Annual Review of Biophysics and Biomolecular Structure. 26: 181-222. PMID 9241418 DOI: 10.1146/Annurev.Biophys.26.1.181  0.332
1997 Ramachandran G, Schlick T. Buckling transitions in superhelical DNA: Dependence on the elastic constants and DNA size Biopolymers. 41: 5-25. PMID 8986117 DOI: 10.1002/(Sici)1097-0282(199701)41:1<5::Aid-Bip2>3.0.Co;2-Y  0.366
1997 Jian H, Vologodskii AV, Schlick T. A combined wormlike-chain and bead model for dynamic simulations of long linear DNA Journal of Computational Physics. 136: 168-179. DOI: 10.1006/Jcph.1997.5765  0.379
1996 Mishra B, Schlick T. The notion of error in Langevin dynamics. I. Linear analysis Journal of Chemical Physics. 105: 299-318. DOI: 10.1063/1.471875  0.315
1995 Schlick T. Modeling superhelical DNA: recent analytical and dynamic approaches Current Opinion in Structural Biology. 5: 245-262. PMID 7648328 DOI: 10.1016/0959-440X(95)80083-2  0.384
1995 Derreumaux P, Schlick T. Long timestep dynamics of peptides by the dynamics driver approach Proteins: Structure, Function and Genetics. 21: 282-302. PMID 7567951 DOI: 10.1002/Prot.340210403  0.33
1995 Ramachandran G, Schlick T. Solvent effects on supercoiled DNA dynamics explored by Langevin dynamics simulations Physical Review E. 51: 6188-6203. DOI: 10.1103/Physreve.51.6188  0.389
1995 Schlick T, Peskin CS. Comment on ‘‘Backward Euler and other methods for simulating molecular fluids’’ [J. Chem. Phys. 103, 3718 (1995)] Journal of Chemical Physics. 103: 9888-9889. DOI: 10.1063/1.469958  0.54
1995 Schlick T, Peskin CS. Comment on "backward Euler and other methods for simulating molecular fluids" [J. Chem. Phys. 103, 3718 (1995)] The Journal of Chemical Physics. 103: 9888-9889.  0.469
1994 Schlick T, Olson WK, Westcott T, Greenberg JP. On higher buckling transitions in supercoiled DNA. Biopolymers. 34: 565-97. PMID 8003619 DOI: 10.1002/Bip.360340502  0.402
1994 Schlick T, Li B, Olson WK. The influence of salt on the structure and energetics of supercoiled DNA. Biophysical Journal. 67: 2146-66. PMID 7696459 DOI: 10.1016/S0006-3495(94)80732-5  0.395
1994 Derreumaux P, Zhang G, Schlick T, Brooks B. A truncated Newton minimizer adapted for CHARMM and biomolecular applications Journal of Computational Chemistry. 15: 532-552. DOI: 10.1002/Jcc.540150506  0.304
1992 Schlick T, Olson WK. Supercoiled DNA energetics and dynamics by computer simulation. Journal of Molecular Biology. 223: 1089-119. PMID 1538391 DOI: 10.1016/0022-2836(92)90263-J  0.425
1992 Schlick T, Olson WK. Trefoil knotting revealed by molecular dynamics simulations of supercoiled DNA. Science (New York, N.Y.). 257: 1110-5. PMID 1509261 DOI: 10.1126/Science.257.5073.1110  0.412
1992 Schlick T, Fogelson A. Algorithm 702: TNPACK–a truncated Newton minimization package for large-scale problems Acm Transactions On Mathematical Software (Toms). 18: 141. DOI: 10.1145/146847.146921  0.586
1992 Schlick T, Fogelson A. TNPACK—a truncated Newton minimization package for large-scale problems Acm Transactions On Mathematical Software (Toms). 18: 71-111. DOI: 10.1145/128745.150975  0.566
1992 Schlick T, Fogelson A. TNPACK—A truncated Newton minimization package for large-scale problems Acm Transactions On Mathematical Software (Toms). 18: 46-70. DOI: 10.1145/128745.150973  0.587
1991 Schlick T, Figueroa S, Mezei M. A molecular dynamics simulation of a water droplet by the implicit‐Euler/Langevin scheme The Journal of Chemical Physics. 94: 2118-2129. DOI: 10.1063/1.459935  0.3
1991 Schlick T. New approaches to potential energy minimization and molecular dynamics algorithms Computers & Chemistry. 15: 251-260. DOI: 10.1016/0097-8485(91)80014-D  0.309
1989 Schlick T, Peskin CS. Can classical equations simulate quantum-mechanical behavior? a molecular dynamics investigation of a diatomic molecule with a morse potential Communications On Pure and Applied Mathematics. 42: 1141-1163. DOI: 10.1002/Cpa.3160420807  0.552
1989 Peskin CS, Schlick T. Molecular dynamics by the Backward-Euler method Communications On Pure and Applied Mathematics. 42: 1001-1031. DOI: 10.1002/Cpa.3160420706  0.527
1987 Schlick T, Peskin C, Broyde S, Overton M. An analysis of the structural and energetic properties of deoxyribose by potential energy methods Journal of Computational Chemistry. 8: 1199-1224. DOI: 10.1002/Jcc.540080817  0.574
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