Schlick, Tamar - Department of Chemistry, New York University

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Schlick, Tamar - Department of Chemistry, New York University

COSTBI-886; NO. OF PAGES 13 Please cite this article in press as: Laing C, Schlick T. Computational approaches to RNA structure prediction, analysis, and design, Curr Opin Struct Biol (2011), doi:10.1016/j.sbi.2011.03.015
Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules
Dynamics of site juxtaposition in supercoiled DNA Jing Huang*
Accessibility of Deoxyribose Protons and Cleavage by Hydroxyl Radical
Tamar Schlick * The Howard Hughes Buckling Transitions in
Deoxyadenosine sugar puckering pathway simulated by the stochastic difference equation algorithm
Inertial stochastic dynamics. II. Influence of inertia on slow kinetic processes of supercoiled DNA
Mismatched Base-Pair Simulations for ASFV Pol X/DNA Complexes Help Interpret Frequent
Subscriber access provided by NEW YORK UNIV Journal of the American Chemical Society is published by the American Chemical
Mathematical and Biological Scientists Assess the State-of-the-Art in RNA Science at an IMA Workshop RNA in Biology, Bioengineering and
Supplemental Data Polymerase fi Simulations Reveal That Arg258
New splitting formulations for lattice summations Paul F. Batchoa)
March 23, 1997 GEOMETRY OPTIMIZATION
Optimization in Computational Chemistry and Molecular Biology, pp. ??-?? C. A. Floudas and P. M. Pardalos, Editors
Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs
EFFICIENT IMPLEMENTATION OF THE TRUNCATEDNEWTON ALGORITHM FOR LARGESCALE CHEMISTRY APPLICATIONS \Lambda
Generating folded protein structures with a lattice chain growth algorithm Hin Hark Gana)
Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration
Biophysical Journal Volume 85 July 2003 14 1 New and Notable
The Loop Opening/Closing Motion of the Enzyme Triosephosphate Isomerase
Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure
Stereochemistry and Position-Dependent Effects of Carcinogens on TATA/TBP Binding
Subscriber access provided by NEW YORK UNIV The Journal of Physical Chemistry A is published by the American Chemical
Fidelity Discrimination in DNA Polymerase : Differing Closing Profiles for a Mismatched (G:A) versus Matched (G:C)
Conformational Transition Pathway of Polymerase /DNA upon Binding Correct Incoming Karunesh Arora and Tamar Schlick*
Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2
Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase l
Journal of Computational Physics 151, 948 (1999) Article ID jcph.1998.6182, available online at http://www.idealibrary.com on
BioMed Central Page 1 of 9
Efficient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations
Structural Motifs in Ribosomal RNAs
From Macroscopic to Mesoscopic Models of Chromatin Folding Tamar Schlick
Local Deformations Revealed by Dynamics Simulations of DNA Polymerase b with DNA
A-Tract Bending: Insights into Experimental Structures by Computational Models
Modular RNA architecture revealed by computational analysis of existing pseudoknots and
We especially need imagination in science. It is not all mathe-matics, nor all logic, but is somewhat beauty and poetry.
Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path
Mesoscale simulations of two nucleosome-repeat length oligonucleosomesw
Candidates for Novel RNA Topologies Namhee Kim1
Modeling Salt-Mediated Electrostatics of
Modeling DNA Polymerase m Motions: Subtle Transitions before Chemistry Yunlang Li and Tamar Schlick*
Supplementary Table: Comparison between termination efficiencies and their computational predicated values. Termination efficiencies are reported in terms of the degree of gene silencing in the
A Quantum Mechanical Investigation of Possible Mechanisms for the Nucleotidyl Transfer Reaction Catalyzed by DNA Polymerase
Invited Talk Searching for 2D RNA Geometries in Bacterial Genomes
Laing and Schlick 27 FIGURE LEGENDS
March 28, 1999 Preface, Special JCP Volume in Computational Molecular Biophysics
Biomolecular Dynamics 1 Long-Timestep Biomolecular Dynamics
Tertiary Motifs Revealed in Analyses of Higher-Order RNA Junctions
June 10, 2003 Deformations of Promoter DNA Bound to Carcinogens Help
Computational generation and screening of RNA motifs in large nucleotide sequence pools
Constructing Irregular Surfaces to Enclose Macromolecular Complexes for Mesoscale Modeling Using the Discrete
Supplementary Information Extended Description of MD Simulation Results
Analysis of Protein Sequence/Structure Similarity Relationships Hin Hark Gan,*
December 22, 2003 Contributed chapter to Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications, J. T. L. Wang,
Chromatin Modeling --supplement 1 Mathematical Model for Structure and Dynamics of Chromatin Supplementary
Supporting Material Replica Exchange Molecular Dynamics (REMD)
Regulation of DNA Repair Fidelity by Molecular Checkpoints: "Gates" in DNA Polymerase 's Substrate Selection
Biophysical Journal, Volume 99 Supporting Material
Critical Role of Magnesium Ions in DNA Polymerase 's Closing and Active Site Assembly
Biophysical Journal Volume 85 November 2003 29732976 2973 Unbiased Rotational Moves for Rigid-Body Dynamics
EFFICIENT IMPLEMENTATION OF THE TRUNCATED-NEWTON ALGORITHM FOR LARGE-SCALE CHEMISTRY APPLICATIONS
Journal of Computational Physics 151, 74113 (1999) Article ID jcph.1999.6202, available online at http://www.idealibrary.com on
Chromatin Modeling ---supplement 1 Mathematical Model for Structure and Dynamics of Chromatin Supplementary
Internal Motion of Supercoiled DNA: Brownian Dynamics Simulations of Site Juxtaposition
A New Program for Optimizing Periodic Boundary Models of Solvated
10.1261/rna.374907Access the most recent version at doi: 2007 13: 478-492; originally published online Feb 23, 2007;RNA
Optimization Methods and Software, Vol. 00, pp. 118 A MORE LENIENT STOPPING RULE
Analysis of Riboswitch Structure and Function by an Energy Landscape Framework
March 23, 1997 GEOMETRY OPTIMIZATION \Lambda
March 28, 1999 Preface, Special JCP Volume in Computational Molecular Biophysics
DNA Pol 's Extraordinary Ability To Stabilize Misaligned Meredith C. Foley,
Laing and Schlick 2 RNA secondary structures can be divided into helical regions composed of canonical Watson-
Relationship Between Conformational Changes in Pol 's Active Site Upon Binding Incorrect Nucleotides and Mismatch Incorporation Rates
Bioinformatics and Biology Insights 2008:2 7795 77 ORIGINAL RESEARCH
In Silico Studies of the African Swine Fever Virus DNA Polymerase X Support an Induced-Fit Mechanism
10.1098/rsta.2004.1386 Deformations of promoter DNA bound to
Biomolecular free energy profiles by a shootingumbrella sampling protocol, ``BOLAS''
Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design
Extrapolation versus impulse in multiple-timestepping schemes. II. Linear analysis and applications to Newtonian and Langevin dynamics
Biomolecularmodelingandsimulation:afield comingofage
1 Modeling Studies of Chromatin Fiber Structure as a 2 Function of DNA Linker Length
BIOINFORMATICS In vitro RNA random pools are not structurally diverse
Macroscopic modeling and simulations of supercoiled DNA with bound proteins
Polymerase bbb Simulations Suggest That Arg258 Rotation is a Slow Step Rather Than Large
Dynamic Simulations of 13 TATA Variants Refine Kinetic Hypotheses of Sequence/Activity
Lattice Protein Folding With Two and Four-Body Statistical Hin Hark Gan,1
he venerable deoxyribonucleic acid molecule has not always held the
Remark on Algorithm 702|The Updated Truncated Newton Minimization Package
Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN
JOURNAL OF COMPUTATIONAL PHYSICS 136, 168179 (1997) ARTICLE NO. CP975765
A FAMILY OF SYMPLECTIC INTEGRATORS: STABILITY, ACCURACY, AND MOLECULAR DYNAMICS APPLICATIONS
J. theor. Biol. (1996) 182, 505512 00225193/96/200505 + 08 $25.00/0 7 1996 Academic Press Limited
Optimized particle-mesh Ewaldmultiple-time step integration for molecular dynamics simulations
The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org 1 RAGPOOLS: RNA-As-Graph-Pools A Web Server for Assisting the
Electrostatic mechanism of nucleosomal array folding revealed by computer simulation
Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions
Supporting Information Supplementary Figure Legends
Chromatin Ionic Atmosphere Analyzed by a Mesoscale Electrostatic Hin Hark Gan
Inertial stochastic dynamics. I. Long-time-step methods for Langevin dynamics
Approaches to RNA 3D modeling 1 Computational approaches to RNA 3D modeling
Sequential Side-Chain Residue Motions Transform the Binary into the Ternary State of DNA Polymerase l
A-Tract Bending: Insights into Experimental Structures by Computational Models
DNA Polymerase Catalysis: Are Different Mechanisms Ian L. Alberts, Yanli Wang, and Tamar Schlick*
10.1261/rna.1249208Access the most recent version at doi: 2008 14: 2465-2477 originally published online October 28, 2008RNA
BIOINFORMATICS Vol. 20 no. 8 2004, pages 12851291
August 25, 2010, Prepared for Quarterly Reviews of Biophysics Biomolecular Modeling and Simulation: A Field
An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization
Subscriber access provided by NEW YORK UNIV Journal of the American Chemical Society is published by the American Chemical
Optimization in Computational Chemistry and Molecular Biology, pp. ???? C. A. Floudas and P. M. Pardalos, Editors
Correct and incorrect nucleotide incorporation pathways in DNA polymerase b
A Hoogsteen base pair embedded in undistorted Jun Aishima1
18 Update November/December 2005 www.nyas.org N A T U R A L I S M I N T H E C O M P U T E R A G E
Modeling studies of chromatin fiber structure as a function of DNA linker length
Mismatch-Induced Conformational Distortions in Polymerase Support an Induced-Fit Mechanism for Fidelity
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Highly Organized but Pliant Active Site of DNA Polymerase b: Compensatory Mechanisms in Mutant Enzymes Revealed by
Differing Conformational Pathways Before and After Chemistry for Insertion of dATP versus dCTP Opposite 8-OxoG in DNA Polymerase b
Supporting Information Regulation of DNA Repair Fidelity by Molecular
Flexible Histone Tails in a New Mesoscopic Oligonucleosome Model Gaurav Arya, Qing Zhang, and Tamar Schlick
804 Biophysical Journal Volume 85 August 2003 804817 Effect of DNA Superhelicity and Bound Proteins on Mechanistic
Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model Gaurav Arya, and Tamar Schlick
In Silico Evidence for DNA Polymerase-b's Substrate-Induced Conformational Change
Remark on Algorithm 702---The Updated Truncated Newton Minimization Package
METHODS AND APPLICATIONS OF ANALYSIS. c 2000 International Press
The notion of error in Langevin dynamics. I. Linear analysis Bimal Mishra and Tamar Schlicka)
Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo
ORIGINAL PAPER A computational screen for C/D box snoRNAs in the human
DATABASE Open Access RAG: An update to the RNA-As-Graphs resource
From SIAM News, Volume 44, Number 6, July/August 2011 By Tamar Schlick and Rosana Collepardo-Guevara
November 23, 2011 Tamar Schlick