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List of works by Tamar Schlick

"Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides

scientific article

A Hoogsteen base pair embedded in undistorted B-DNA.

scientific article

A computational proposal for designing structured RNA pools for in vitro selection of RNAs

scientific article published on 23 February 2007

A computational screen for C/D box snoRNAs in the human genomic region associated with Prader-Willi and Angelman syndromes

scientific article published on 27 July 2008

A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID).

scientific article

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).

scientific article

A pipeline for computational design of novel RNA-like topologies.

scientific article published in August 2018

A quantum mechanical investigation of possible mechanisms for the nucleotidyl transfer reaction catalyzed by DNA polymerase beta

scientific article

A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments

scientific article published in April 2009

ANERGY TO SYNERGY-THE ENERGY FUELING THE RXCOVEA FRAMEWORK

scientific article published on 01 January 2020

Adventures with RNA graphs

scientific article published on 2 April 2018

Algorithm 702: TNPACK–a truncated Newton minimization package for large-scale problems

scientific article published on 27 July 2002

An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures

scientific article published on 27 March 2019

Analysis of four-way junctions in RNA structures

scientific article published on 13 May 2009

Analysis of protein sequence/structure similarity relationships

scientific article

Analysis of riboswitch structure and function by an energy landscape framework

scientific article published on 3 September 2009

Annotation of tertiary interactions in RNA structures reveals variations and correlations

scientific article published on 28 October 2008

Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS"

scientific article

Biomolecularmodeling and simulation: a field coming of age.

scientific article published on May 2011

Buckling transitions in superhelical DNA: dependence on the elastic constants and DNA size

scientific article published in January 1997

CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking

scientific article published on 20 January 2016

Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site

scientific article published on 28 December 2012

Candidates for novel RNA topologies

scientific article

Challenges in RNA Structural Modeling and Design

scientific article

Chromatin Fiber Folding Directed by Cooperative Histone Tail Acetylation and Linker Histone Binding

scientific article published on 11 April 2018

Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study

scientific article

Chromatin fiber polymorphism triggered by variations of DNA linker lengths

scientific article

Chromatin ionic atmosphere analyzed by a mesoscale electrostatic approach

scientific article

Cohesin Loss Eliminates All Loop Domains

scientific article published in October 2017

Computational approaches to 3D modeling of RNA.

scientific article published on 15 June 2010

Computational approaches to RNA structure prediction, analysis, and design

scientific article published on 21 April 2011

Computational generation and screening of RNA motifs in large nucleotide sequence pools

scientific article

Computational modeling predicts the structure and dynamics of chromatin fiber

scientific article

Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP: a hierarchical graph sampling approach

scientific article published on 7 February 2015

Computational strategies to address chromatin structure problems.

scientific article published on 25 June 2016

Configurational transitions in Fourier series-represented DNA supercoils

scientific article

Conformational transition pathway of polymerase beta/DNA upon binding correct incoming substrate

scientific article

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm

scientific article

Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta

scientific article

Correlation among DNA Linker Length, Linker Histone Concentration, and Histone Tails in Chromatin.

scientific article published on June 2016

Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly

scientific article

Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes

scientific article

DNA pol λ's extraordinary ability to stabilize misaligned DNA.

scientific article

DNA polymerase beta catalysis: are different mechanisms possible?

scientific article

Deformations of promoter DNA bound to carcinogens help interpret effects on TATA-element structure and activity

scientific article

Dependence of the Linker Histone and Chromatin Condensation on the Nucleosome Environment.

scientific article published on 21 July 2017

Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta

scientific article published on 9 February 2007

Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides

scientific article published on 21 February 2007

Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs

scientific article published on 25 July 2018

Dynamic condensation of linker histone C-terminal domain regulates chromatin structure.

scientific article published on 6 June 2014

Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function

scientific article

Effect of DNA superhelicity and bound proteins on mechanistic aspects of the Hin-mediated and Fis-enhanced inversion

scientific article

Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo

scientific article

Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

scientific article

Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry

scientific article published on 12 March 2020

Engineering teams up with computer-simulation and visualization tools to probe biomolecular mechanisms

scientific article published on July 2003

Estimating the fraction of non-coding RNAs in mammalian transcriptomes.

scientific article published on March 2008

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

scholarly article

Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design

scientific article

F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly

scientific article published on 5 October 2017

Fidelity discrimination in DNA polymerase beta: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair

scientific article published in September 2005

Flexible histone tails in a new mesoscopic oligonucleosome model

scientific article

Forced unraveling of chromatin fibers with nonuniform linker DNA lengths

scientific article

Graph-based sampling for approximating global helical topologies of RNA.

scientific article published on 03 March 2014

Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes

scientific article

Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses.

scientific article

How DNA polymerase X preferentially accommodates incoming dATP opposite 8-oxoguanine on the template

scientific article published on December 2013

Identification of novel RNA design candidates by clustering the extended RNA-As-Graphs library

scientific article published on 16 January 2020

In silico evidence for DNA polymerase-beta's substrate-induced conformational change

scientific article

In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanism

scientific article

In vitro RNA random pools are not structurally diverse: a computational analysis

scientific article

Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms

scientific article

Insertion of oxidized nucleotide triggers rapid DNA polymerase opening

scientific article published on 31 March 2016

Insights into chromatin fibre structure by in vitro and in silico single-molecule stretching experiments

scientific article published on April 2013

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

scientific article published on January 2014

Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies

scientific article published on 23 December 2019

Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome Depletion

scientific article published on 16 March 2017

Lattice protein folding with two and four-body statistical potentials.

scientific article

Linking Chromatin Fibers to Gene Folding by Hierarchical Looping

scientific article published on 31 January 2017

Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus

scientific article

Mathematical and Biological Scientists Assess the State of the Art in RNA Science at an IMA Workshop, RNA in Biology, Bioengineering, and Biotechnology

scientific article published in 2010

Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements.

scientific article

Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation

scientific article published on 01 January 2021

Mesoscale Modeling of Nucleosome-Binding Antibody PL2-6: Mono- versus Bivalent Chromatin Complexes

scientific article published on 22 August 2019

Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub

scientific article published on 04 February 2019

Mesoscale simulations of two nucleosome-repeat length oligonucleosomes

scientific article published on 20 October 2009

Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity.

scientific article

Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation

scientific article published on 17 October 2008

Modeling DNA polymerase μ motions: subtle transitions before chemistry

scientific article

Modeling studies of chromatin fiber structure as a function of DNA linker length.

scientific article published on 13 August 2010

Modeling superhelical DNA: recent analytical and dynamic approaches.

scientific article published on April 1995

Modified Cholesky Factorizations for Sparse Preconditioners

scientific article published in 1993

Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs

scientific article

Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules ⬇️

scientific article published on July 8, 2009

Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure ⬇️

scientific article published on June 29, 2009

Multiscale Genome Organization: Dazzling Subject and Inventive Methods

scientific article published on 16 April 2020

Network Theory Tools for RNA Modeling

scientific article

Nucleosome clutches are regulated by chromatin internal parameters

scientific article published on 09 November 2020

Opportunities and Challenges in RNA Structural Modeling and Design

scientific article published on 2 February 2017

Optimal and variant metal-ion routes in DNA polymerase β's conformational pathways

scientific article

Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing

scholarly article

Partitioning and Classification of RNA Secondary Structures into Pseudonotted and Pseudoknot-free Regions Using a Graph-Theoretical Approach

scientific article published on 24 May 2017

Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms

scientific article published on 23 November 2012

Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se.

scientific article published on April 2002

Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach

scientific article published on 15 October 2015

Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs

scientific article

Predicting coaxial helical stacking in RNA junctions

scientific article published on 14 September 2011

Predicting helical topologies in RNA junctions as tree graphs

scientific article

Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization

scientific article published on 12 September 2008

RAG-3D: a search tool for RNA 3D substructures

scientific article

RAG-Web: RNA structure prediction/design using RNA-As-Graphs

scientific article published on 01 January 2020

RAG: RNA-As-Graphs database--concepts, analysis, and features

scientific article

RAG: RNA-As-Graphs web resource

scientific article

RAG: an update to the RNA-As-Graphs resource

scientific article

RNA Structural Variability and Functional Versatility Challenge RNA Structural Modeling and Design

scientific article published on 29 June 2017

RNA graph partitioning for the discovery of RNA modularity: a novel application of graph partition algorithm to biology

scientific article

RagPools: RNA-As-Graph-Pools--a web server for assisting the design of structured RNA pools for in vitro selection

scientific article

Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection

scientific article

Relationship between conformational changes in pol lambda's active site upon binding incorrect nucleotides and mismatch incorporation rates

scientific article published on October 2009

Remark on Algorithm 566

scientific article published on 27 July 2002

Remark on Algorithm 702—the updated truncated Newton minimization package

scientific article published on 27 July 2002

Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model

scholarly article

Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations

scientific article published on 17 April 2019

Sensitive effect of linker histone binding mode and subtype on chromatin condensation.

scientific article

Sequence-dependent solution structure and motions of 13 TATA/TBP (TATA-box binding protein) complexes

scientific article

Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda

scientific article

Simulations of DNA pol lambda R517 mutants indicate 517's crucial role in ternary complex stability and suggest DNA slippage origin

scientific article

Stereochemistry and position-dependent effects of carcinogens on TATA/TBP binding

scientific article

Structural motifs in ribosomal RNAs: implications for RNA design and genomics

scientific article published on February 2004

Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element

scientific article published on 30 August 2020

Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element

scientific article published on 20 October 2020

Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase λ

scientific article

Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass

scientific article published on December 2005

Supercoiled DNA energetics and dynamics by computer simulation

scientific article published on February 1992

TNPACK—A truncated Newton minimization package for large-scale problems

scientific article published on 27 July 2002

TNPACK—a truncated Newton minimization package for large-scale problems

scientific article published on 27 July 2002

Tertiary motifs revealed in analyses of higher-order RNA junctions

scientific article published on 03 August 2009

The chromatin fiber: multiscale problems and approaches

scientific article published on April 2015

The effect of linker histone's nucleosome binding affinity on chromatin unfolding mechanisms.

scientific article

The influence of salt on the structure and energetics of supercoiled DNA

scientific article

The loop opening/closing motion of the enzyme triosephosphate isomerase

scientific article

Time-trimming tricks for dynamic simulations: splitting force updates to reduce computational work

scientific article

To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element

scientific article published on 20 July 2021

Toward convergence of experimental studies and theoretical modeling of the chromatin fiber

scientific article

Trefoil knotting revealed by molecular dynamics simulations of supercoiled DNA

scientific article published on August 21, 1992

Unbiased rotational moves for rigid-body dynamics

scientific article published on November 2003

Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide

scientific article

Unfavorable Electrostatic and Steric Interactions in DNA Polymerase β E295K Mutant Interfere with the Enzyme’s Pathway

scientific article

Unraveling Genome Biophysics

scientific article published on 18 January 2017

Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction

scientific article

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