Tamar Schlick

Q: What Schools Are Affiliated With Tamar Schlick

Tamar Schlick is affiliated with the following schools: University of California, Berkeley, Weizmann Institute of Science, Wayne State University, New York University

Tamar Schlick's AcademicInfluence.com Rankings

Tamar Schlick

Mathematics

#3025

World Rank

#4548

Historical Rank

#1148

USA Rank

Measure Theory

#1209

World Rank

#1537

Historical Rank

#439

USA Rank

mathematics Degrees

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Mathematics

Tamar Schlick's Degrees

PhD Mathematics University of California, Berkeley

Why Is Tamar Schlick Influential?

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According to Wikipedia, Tamar Schlick is an American applied mathematician who works as a professor of chemistry, mathematics, and computer science at New York University. Her research involves developing and applying tools for modeling and simulating biomolecules.

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Tamar Schlick's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Cohesin Loss Eliminates All Loop Domains (2017) (1140)
Molecular Modeling and Simulation: An Interdisciplinary Guide (2010) (716)
Molecular modeling and simulation (2002) (426)
Lecture Notes in Computational Science and Engineering (2015) (238)
Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions (2009) (236)
Algorithmic Challenges in Computational Molecular Biophysics (1999) (203)
Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations (2001) (191)
Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. (2003) (173)
Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model (2006) (164)
Modeling superhelical DNA: recent analytical and dynamic approaches. (1995) (155)
A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments. (2009) (144)
Computational approaches to RNA structure prediction, analysis, and design. (2011) (143)
Numerical Experience with Limited-Memory Quasi-Newton and Truncated Newton Methods (1993) (140)
Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing. (2004) (134)
Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly. (2004) (133)
Biomolecular dynamics at long timesteps: bridging the timescale gap between simulation and experimentation. (1997) (133)
Supercoiled DNA energetics and dynamics by computer simulation. (1992) (129)
Biomolecular modeling and simulation: a field coming of age (2011) (128)
A Combined Wormlike-Chain and Bead Model for Dynamic Simulations of Long Linear DNA (1997) (126)
A Family of Symplectic Integrators: Stability, Accuracy, and Molecular Dynamics Applications (1997) (125)
TNPACK—A truncated Newton minimization package for large-scale problems: I. Algorithm and usage (1992) (123)
The influence of salt on the structure and energetics of supercoiled DNA. (1994) (122)
Uncovering the Polymerase-induced Cytotoxicty of an Oxidized Nucleotide (2014) (120)
A-Tract bending: insights into experimental structures by computational models. (2000) (119)
Computational approaches to 3D modeling of RNA (2010) (111)
Chromatin fiber polymorphism triggered by variations of DNA linker lengths (2014) (110)
Electrostatic mechanism of nucleosomal array folding revealed by computer simulation. (2005) (110)
Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study. (2015) (108)
Trefoil Knotting Revealed by Molecular Dynamics Simulations of Supercoiled DNA (1992) (106)
Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes (2016) (104)
Analysis of four-way junctions in RNA structures. (2009) (102)
Computational modeling predicts the structure and dynamics of chromatin fiber. (2001) (100)
Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture (2020) (98)
Internal motion of supercoiled DNA: brownian dynamics simulations of site juxtaposition. (1998) (98)
Flexible histone tails in a new mesoscopic oligonucleosome model. (2006) (96)
Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN (1998) (93)
Dynamics of site juxtaposition in supercoiled DNA. (2001) (92)
Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome. (2001) (91)
Toward Convergence of Experimental Studies and Theoretical Modeling of the Chromatin Fiber* (2011) (90)
Nonlinear Resonance Artifacts in Molecular Dynamics Simulations (1998) (88)
Modeling studies of chromatin fiber structure as a function of DNA linker length. (2010) (88)
In vitro RNA random pools are not structurally diverse: a computational analysis. (2005) (85)
Analysis of protein sequence/structure similarity relationships. (2002) (84)
Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. (2002) (81)
RAG: RNA-As-Graphs database—concepts, analysis, and features (1987) (80)
Annotation of tertiary interactions in RNA structures reveals variations and correlations. (2008) (77)
Extrapolation versus impulse in multiple-timestepping schemes. II. Linear analysis and applications to Newtonian and Langevin dynamics (1998) (75)
RAG: RNA-As-Graphs web resource (2004) (75)
The loop opening/closing motion of the enzyme triosephosphate isomerase. (1998) (74)
Molecular dynamics by the backward-Euler method (1989) (69)
Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection. (2006) (68)
A Hoogsteen base pair embedded in undistorted B-DNA. (2002) (65)
Engineering teams up with computer-simulation and visualization tools to probe biomolecular mechanisms. (2003) (65)
The chromatin fiber: multiscale problems and approaches. (2015) (63)
LIN: A new algorithm to simulate the dynamics of biomolecules by combining implicit‐integration and normal mode techniques (1993) (63)
TNPACK—a truncated Newton minimization package for large-scale problems: II. Implementation examples (1992) (61)
Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations (2019) (61)
Resonance in the dynamics of chemical systems simulated by the implicit midpoint scheme (1995) (61)
Fidelity discrimination in DNA polymerase beta: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair. (2005) (61)
Predicting coaxial helical stacking in RNA junctions (2011) (57)
Graph-based sampling for approximating global helical topologies of RNA (2014) (57)
Candidates for novel RNA topologies. (2004) (57)
DNA Polymerase β Catalysis: Are Different Mechanisms Possible? (2007) (56)
Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules (2009) (55)
Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm (2003) (53)
A computational proposal for designing structured RNA pools for in vitro selection of RNAs. (2007) (53)
Dynamic condensation of linker histone C-terminal domain regulates chromatin structure (2014) (53)
Tertiary motifs revealed in analyses of higher-order RNA junctions. (2009) (52)
A truncated Newton minimizer adapted for CHARMM and biomolecular applications (1994) (52)
Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta. (2006) (51)
Efficient Implementation of the Truncated-Newton Algorithm for Large-Scale Chemistry Applications (1999) (51)
The Langevin/implicit‐Euler/normal‐mode scheme for molecular dynamics at large time steps (1994) (51)
Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS". (2004) (50)
Lattice protein folding with two and four‐body statistical potentials (2001) (50)
Opportunities and Challenges in RNA Structural Modeling and Design. (2017) (49)
Translational and vibrational energy dependence of the cross section for H + C2H4 .fwdarw. C2H5* (1981) (49)
Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus. (2002) (48)
New Algorithms for Macromolecular Simulation (2006) (48)
RAG: An update to the RNA-As-Graphs resource (2011) (47)
Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity. (2005) (47)
In silico evidence for DNA polymerase-beta's substrate-induced conformational change. (2004) (47)
Geometry Optimization: 2 (2002) (46)
RAG: RNA-As-Graphs database-concepts, analysis, features (2004) (46)
Supporting Material (2006) (45)
Time-trimming tricks for dynamic simulations: splitting force updates to reduce computational work. (2001) (44)
Innovations in Biomolecular Modeling and Simulations (2012) (43)
Computational Methods for Macromolecules: Challenges and Applications (2002) (42)
Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses. (2004) (41)
Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub (2019) (41)
Unbiased rotational moves for rigid-body dynamics. (2003) (41)
Mesoscale simulations of two nucleosome-repeat length oligonucleosomes. (2009) (40)
Masking Resonance Artifacts in Force-Splitting Methods for Biomolecular Simulations by Extrapolative Langevin Dynamics (1999) (40)
Linking Chromatin Fibers to Gene Folding by Hierarchical Looping. (2017) (39)
Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization. (2008) (39)
Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes (2012) (38)
Efficient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations (2002) (38)
Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms (2012) (38)
THE NOTION OF ERROR IN LANGEVIN DYNAMICS. I. LINEAR ANALYSIS (1996) (37)
Macroscopic modeling and simulations of supercoiled DNA with bound proteins (2002) (37)
Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function (2012) (37)
Inertial stochastic dynamics. I. Long-time-step methods for Langevin dynamics (2000) (37)
On higher buckling transitions in supercoiled DNA (1994) (37)
Predicting Helical Topologies in RNA Junctions as Tree Graphs (2013) (35)
Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs (2005) (35)
Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase λ (2008) (35)
Modified Cholesky Factorizations for Sparse Preconditioners (1993) (35)
Computational generation and screening of RNA motifs in large nucleotide sequence pools (2010) (34)
Multiplicative Operator Splittings in Nonlinear Diffusion: From Spatial Splitting to Multiple Timesteps (2003) (34)
Adventures with RNA graphs. (2018) (34)
Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements. (2016) (33)
Sensitive effect of linker histone binding mode and subtype on chromatin condensation (2019) (32)
Analysis of riboswitch structure and function by an energy landscape framework. (2009) (32)
A quantum mechanical investigation of possible mechanisms for the nucleotidyl transfer reaction catalyzed by DNA polymerase beta. (2007) (32)
The effect of linker histone's nucleosome binding affinity on chromatin unfolding mechanisms. (2011) (32)
Implicit discretization schemes for Langevin dynamics (1995) (31)
Computational challenges in simulating large DNA over long times (2000) (31)
Pursuing Laplace's vision on modern computers (1996) (31)
Modeling biomolecules: larger scales, longer durations (1994) (31)
Deoxyadenosine sugar puckering pathway simulated by the stochastic difference equation algorithm (2003) (31)
F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly. (2017) (30)
Faculty Opinions recommendation of Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family. (2010) (30)
Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site (2012) (30)
Network Theory Tools for RNA Modeling. (2013) (30)
Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration (2001) (30)
Dynamic simulations of 13 TATA variants refine kinetic hypotheses of sequence/activity relationships. (2001) (29)
RAGPOOLS: RNA-As-Graph-Pools - a web server for assisting the design of structured RNA pools for in vitro selection (2007) (29)
Can classical equations simulate quantum‐mechanical behavior? a molecular dynamics investigation of a diatomic molecule with a morse potential (1989) (29)
Publisher Correction: Biomolecular modeling thrives in the age of technology (2021) (28)
Inertial stochastic dynamics. II. Influence of inertia on slow kinetic processes of supercoiled DNA (2000) (28)
Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation (2021) (28)
Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms (2003) (27)
RAG-3D: a search tool for RNA 3D substructures (2015) (27)
Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element (2020) (25)
Optimization Methods in Computational Chemistry (2007) (25)
An analysis of the structural and energetic properties of deoxyribose by potential energy methods (1987) (24)
Conformational transition pathway of polymerase beta/DNA upon binding correct incoming substrate. (2005) (24)
A molecular dynamics simulation of a water droplet by the implicit-Euler/Langevin scheme (1991) (24)
Distinct energetics and closing pathways for DNA polymerase β with 8-oxoG template and different incoming nucleotides (2007) (23)
New splitting formulations for lattice summations (2001) (23)
An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization (2000) (23)
Graph Applications to RNA Structure and Function (2013) (22)
Long timestep dynamics of peptides by the dynamics driver approach (1995) (22)
Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs (2005) (22)
Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass (2006) (22)
Increasing the time step in molecular dynamics (1992) (22)
Remark on Algorithm 702—the updated truncated Newton minimization package (1999) (22)
A pipeline for computational design of novel RNA-like topologies (2018) (21)
Molecular modeling: An interdisciplinary guide (2010) (21)
Correlation among DNA Linker Length, Linker Histone Concentration, and Histone Tails in Chromatin. (2016) (21)
Chromatin ionic atmosphere analyzed by a mesoscale electrostatic approach. (2010) (21)
Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP: a hierarchical graph sampling approach. (2015) (21)
Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction (2017) (20)
Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry (2020) (20)
Chromatin Fiber Folding Directed by Cooperative Histone Tail Acetylation and Linker Histone Binding. (2018) (20)
Computational Molecular Biophysics Today (1999) (19)
Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta. (2007) (19)
Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome Depletion. (2017) (19)
RNA Graph Partitioning for the Discovery of RNA Modularity: A Novel Application of Graph Partition Algorithm to Biology (2014) (19)
Stereochemistry and position-dependent effects of carcinogens on TATA/TBP binding. (2006) (19)
Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations (1999) (18)
Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway. (2012) (18)
Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation. (2008) (17)
Sequence‐dependent solution structure and motions of 13 TATA/TBP (TATA‐box binding protein) complexes (2003) (17)
Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo. (2007) (17)
Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field. (2021) (17)
To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element (2021) (17)
A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID) (2001) (17)
Nucleosome clutches are regulated by chromatin internal parameters. (2020) (16)
A transition-rate investigation by molecular dynamics with the Langevin/implicit-Euler scheme (1991) (16)
A recipe for evaluating and differentiating cos ϕ expressions (1989) (16)
Dependence of the Linker Histone and Chromatin Condensation on the Nucleosome Environment. (2017) (16)
Buckling transitions in superhelical DNA: dependence on the elastic constants and DNA size. (1997) (16)
Generating folded protein structures with a lattice chain growth algorithm (2000) (15)
Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling (2020) (15)
Modeling DNA polymerase μ motions: subtle transitions before chemistry. (2010) (15)
Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda. (2006) (15)
A separating framework for increasing the timestep in molecular dynamics (1997) (15)
A computational screen for C/D box snoRNAs in the human genomic region associated with Prader-Willi and Angelman syndromes. (2008) (15)
Challenges in RNA Structural Modeling and Design. (2016) (15)
In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanism. (2006) (14)
Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach. (2016) (14)
Computational strategies to address chromatin structure problems (2016) (13)
To knot or not to knot: Multiple conformations of the SARS-CoV-2 frameshifting RNA element (2021) (13)
An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures. (2019) (13)
An adaptive multigrid technique for evaluating long-range forces in biomolecular simulations (1998) (12)
Inverse Folding with RNA-As-Graphs Produces a Large Pool of Candidate Sequences with Target Topologies. (2019) (12)
DNA polymerase beta catalysis: are different mechanisms possible? (2007) (12)
Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure (2009) (12)
Visualization of Chemical Databases Using the Singular Value Decomposition and Truncated-Newton Minimization (2000) (12)
A More Lenient Stopping Rule for Line Search Algorithms (2002) (12)
Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs (2018) (12)
A Multigrid Tutorial with Applications to Molecular Dynamics (1996) (11)
Molecular Dynamics: Basics (2010) (11)
5 – Mesoscale Modeling of Chromatin Fibers (2018) (11)
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. (2014) (11)
The 2013 Nobel Prize in Chemistry Celebrates Computations in Chemistry and Biology (2013) (11)
New Algorithms for Macromolecular Simulation (Lecture Notes in Computational Science and Engineering) (2006) (11)
“Gate-keeper” Residues and Active-Site Rearrangements in DNA Polymerase μ Help Discriminate Non-cognate Nucleotides (2013) (10)
Insights into chromatin fibre structure by in vitro and in silico single-molecule stretching experiments. (2013) (9)
Optimal and variant metal-ion routes in DNA polymerase β's conformational pathways. (2014) (9)
Comment on ‘‘Backward Euler and other methods for simulating molecular fluids’’ [J. Chem. Phys. 103, 3718 (1995)] (1995) (9)
Structural motifs in ribosomal RNAs: Implications for RNA design and genomics (2004) (9)
Insertion of oxidized nucleotide triggers rapid DNA polymerase opening (2016) (8)
Partitioning and Classification of RNA Secondary Structures into Pseudonotted and Pseudoknot-free Regions Using a Graph-Theoretical Approach. (2017) (8)
Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model (1996) (7)
Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells (2021) (7)
Simulations of DNA pol lambda R517 mutants indicate 517's crucial role in ternary complex stability and suggest DNA slippage origin. (2008) (7)
Relationship between conformational changes in pol lambda's active site upon binding incorrect nucleotides and mismatch incorporation rates. (2009) (7)
How DNA polymerase X preferentially accommodates incoming dATP opposite 8-oxoguanine on the template. (2013) (7)
Effect of DNA superhelicity and bound proteins on mechanistic aspects of the Hin-mediated and Fis-enhanced inversion. (2003) (7)
Computational approaches to 3 D modeling of RNA (2010) (7)
Remark on Algorithm 566 (1994) (7)
CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking (2016) (7)
Forced unraveling of chromatin fibers with nonuniform linker DNA lengths (2015) (7)
New Approaches to Potential Energy Minimization and Molecular Dynamics Algorithms (1991) (6)
Object-Oriented Analysis and Design (2007) (6)
Partitioning RNAs into pseudonotted and pseudoknot-free regions modeled as Dual Graphs (2016) (6)
Deformations of promoter DNA bound to carcinogens help interpret effects on TATA-element structure and activity (2004) (6)
Special Section On Multiscale Modeling In Biology (2006) (6)
From Macroscopic to Mesoscopic Models of Chromatin Folding (2009) (6)
RAG-Web: RNA structure prediction/design using RNA-As-Graphs (2019) (5)
Ph.D. dissertation: Modeling and minimization techniques for predicting three-dimensional structures of large biological molecules (1987) (5)
Mathematical and Biological Scientists Assess the State-of-the-Art in RNA Science at an IMA Workshop RNA in Biology, Bioengineering and Biotechnology (2010) (5)
A powerful truncated Newton method for potential energy minimization (2018) (5)
Searching for 2D RNA geometries in bacterial genomes (2004) (5)
DNA pol λ's extraordinary ability to stabilize misaligned DNA. (2010) (5)
Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element (2020) (5)
A modular strategy for generating starting conformations and data structures of polynucleotide helices for potential energy calculations (1988) (5)
Analysis of the SHAKE-SOR algorithm for constrained molecular dynamics simulations (2000) (5)
Computational methods for macromolecules: Challenges and applications - Proceedings of the 3rd international workshop on algorithms for macromolecular modelling, New York, October 12-14, 2000 (2002) (5)
Search strategies, minimization algorithms, and molecular dynamics simulations for exploring conformational spaces of nuclear acids (1990) (5)
Configurational transitions in Fourier series-represented DNA supercoils. (1997) (5)
The Critical Collaboration between Art and Science: An Experiment on a Bird in the Air Pump and the Ramifications of Genomics for Society (2005) (4)
Simulations of Dna Pol Ï¿¿ R517 Mutants Indicate 517's Crucial Role in Ternary Complex Stability and Suggest Dna Slippage Origin Simulations of Dna Pol Λ R517 Mutants Indicate 517's Crucial Role in Ternary Complex Stability and Suggest Dna Slippage Origin (4)
Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression (2022) (4)
HESFCN - A Fortran package of Hessian Subroutines for Testing Nonlinear Optimization Software (1992) (4)
Calibration of the timestep for molecular dynamics of supercoiled DNA modeled by B-splines (1994) (4)
Identification of novel RNA design candidates by clustering the extended RNA-as-graphs library. (2020) (4)
Biomolecular Structure and Modeling: Historical Perspective (2010) (4)
RNA: The Cousin Left Behind Becomes a Star (2006) (4)
A MULTISCALE VISION-ILLUSTRATIVE APPLICATIONS FROM BIOLOGY TO ENGINEERING. (2021) (3)
Application of Fourier analysis to computer simulation of supercoiled DNA conformation (1995) (3)
Nucleic Acids Structure Minitutorial (2010) (3)
Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression (2022) (3)
Algorithm 702: TNPACK–a truncated Newton minimization package for large-scale problems: I. Algorithm and usage (1992) (3)
Chapter 4:Intrinsic Motions of DNA Polymerases Underlie Their Remarkable Specificity and Selectivity and Suggest a Hybrid Substrate Binding Mechanism (2012) (3)
A Fiedler Vector Scoring Approach for Novel RNA Motif Selection. (2021) (3)
Differing conformational pathways before and after chemistry for insertion of dATP vs . dCTP opposite 8-oxoG in DNA polymerase β (2007) (3)
Innovations in biomolecular modeling and simulation: Volumes 1 and 2 (2012) (3)
Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells (2020) (3)
Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions (2022) (2)
RNA Structural Variability and Functional Versatility Challenge RNA Structural Modeling and Design. (2017) (2)
Long-timestep biomolecular dynamics simulations: LN performance on a polymerase β/DNA system (2001) (2)
Multivariate Minimization in Computational Chemistry (2010) (2)
Exploring the Connection Between Synthetic and Natural RNAs in Genomes: A Novel Computational Approach (2006) (2)
Mesoscale Modeling of Nucleosome-Binding Antibody PL2-6: Mono- versus Bivalent Chromatin Complexes. (2020) (2)
Theoretical and Computational Approaches to Biomolecular Structure (2010) (2)
Biomolecular modeling thrives in the age of technology (2021) (1)
Molecular Dynamics: Further Topics (2010) (1)
A Simple Solvation Model Along with A Multibody Dynamics Strategy (MBO(N)D) Produces Stable DNA Simulations that are Faster than Traditional Atomistic Methods (2000) (1)
ANERGY TO SYNERGY-THE ENERGY FUELING THE RXCOVEA FRAMEWORK. (2020) (1)
Topics in Nucleic Acids Structure: DNA Interactions and Folding (2010) (1)
Multiscale Genome Organization: Dazzling Subject and Inventive Methods (2020) (1)
Biophysicists’ continued outstanding response to COVID-19 (2021) (1)
Genome modeling: From chromatin fibers to genes. (2022) (1)
Mesoscale Modeling of a Nucleosome-Binding Antibody (PL2-6): Mono- vs. Bivalent Chromatin Complexes (2019) (1)
MGO on the go: Multiscale genome symposium - annual biophysical society meeting 2021 (2021) (1)
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). (2012) (1)
Chromatin transitions triggered by LH density as epigenetic regulators of the genome (2022) (1)
Brownian Dynamics Simulations of Mesoscale Chromatin Fibers. (2022) (1)
Junction-Explorer Help File (2015) (1)
MATALPHA2 HOMEODOMAIN BOUND TO DNA (2002) (1)
A Primer on Scientific Programming with Python Fifth Edition (2020) (1)
Estimating the Fraction of Non-Coding RNAs in Mammalian Transcriptomes (2008) (1)
Similarity and Diversity in Chemical Design (2010) (1)
Conformational transitions in DNA polymerases (2009) (1)
RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications (2022) (1)
Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture (2020) (1)
Eight Suggestions for Future Leaders of Science and Technology. (2020) (1)
Topics in Nucleic Acids Structure: Noncanonical Helices and RNA Structure (2010) (1)
Biomolecular Modeling and Simulation: The Productive Trajectory of a Field (2011) (1)
Graph-based sampling approach for approximating global helical topologies of RNA (2013) (1)
Studies of African Swine Fever Virus Polymerase X/DNA complexes in the presence of mismatched base pairs (2008) (0)
Patterns at Work: Multiple Graphs (2007) (0)
Nucleosome Clutches in Chromatin are Tightly Regulated by Nucleosome Positions and Linker Histone Density (2020) (0)
Chain of Responsibility (2007) (0)
Reinterpreting Joseph Wright's An Experiment on a Bird in the Air Pump in the 21st Century Genomics Revolution (2004) (0)
Biophysicists' outstanding response to Covid-19 (2021) (0)
Computational Genomics Using Graph Theory (2005) (0)
Design Patterns for e-Science (2007) (0)
e-Science and EScope (2007) (0)
A Java Client for MDSplus (2007) (0)
Faculty Opinions recommendation of Two-metal active site binding of a Tn5 transposase synaptic complex. (2002) (0)
Topics in Nucleic Acids Structure (2002) (0)
Faculty Opinions recommendation of RNA mimics of green fluorescent protein. (2011) (0)
Supercoiled configurations of small DNA rings and their dynamics (1993) (0)
Author response: Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells (2021) (0)
Innovations in biophysics: A sampling of ideas celebrating Ned Seeman's legacy. (2022) (0)
Computational molecular biophysics: Special issue (1999) (0)
Protein Structure Hierarchy (2010) (0)
Mesoscale Modeling of Chromatin Folding (2009) (0)
Design Patterns and Threads (2007) (0)
Folding RNA by RAGTOP: RNA-As-Graph-Topologies (2014) (0)
Supporting Information Appendix (2014) (0)
Faculty Opinions recommendation of Condensin-Dependent Chromatin Compaction Represses Transcription Globally during Quiescence. (2019) (0)
Adventures with RNA Graphs (2017) (0)
Invited Talk Searching for 2 D RNA Geometries in Bacterial Genomes (2004) (0)
Faculty Opinions recommendation of In silico selection of RNA aptamers. (2011) (0)
Isabella L. Karle: A Crystallography Pioneer. (2021) (0)
Faculty Opinions recommendation of Dual role of the RNA substrate in selectivity and catalysis by terminal uridylyl transferases. (2007) (0)
DNA polymerases structure, function, and modeling (2011) (0)
Protein Structure Introduction (2010) (0)
Final Report of the M(sup 3) Workshop at NYU, October 12-14, 2000 (2002) (0)
Structure of a ternary complex of the R517K Pol lambda mutant (2008) (0)
Modeling and simulating biomolecules (1997) (0)
Faculty Opinions recommendation of Automated de novo prediction of native-like RNA tertiary structures. (2007) (0)
Faculty Opinions recommendation of Computational approaches toward the design of pools for the in vitro selection of complex aptamers. (2011) (0)
Molecular Machines DNA Polymerases Structure , Function , and Modeling (2011) (0)
Faculty Opinions recommendation of Watching DNA polymerase η make a phosphodiester bond. (2013) (0)
How to simulate the quantum-mechanical suppression of high-frequency modes in classical molecular dynamics computations (1990) (0)
Structural insights into DNA polymerase X from African swine fever virus in the presence of oxoG lesions (2010) (0)
Patterns at Work: Multiple Waves (2007) (0)
Faculty Opinions recommendation of Nuclear lamina integrity is required for proper spatial organization of chromatin in Drosophila. (2019) (0)
Models of conformational selection of DNA polymerase X in the presence of oxoG lesions help interpret kinetics data (2013) (0)
Graphical User Interfaces Using Swing (2007) (0)
Issue Information (2019) (0)
Faculty Opinions recommendation of Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity. (2007) (0)
Interactive Graphics Using Mouse Events (2007) (0)
Analysis of Junctions in RNA with Coaxial Stacked Helices (2012) (0)
Unraveling Genome Biophysics While digitizing the human (0)
Navigating the Database (2007) (0)
Graph-Theoretic Partitioning of RNAs and Classification of Pseudoknots (2019) (0)
Monte Carlo Techniques (2010) (0)
From butterflies to bits: A sweeping vision for the code of life (2021) (0)
Implementation of the Schnabel & Eskow modified Cholesky factorization in the context of large-scale nonlinear optimization (1990) (0)
Time-Trimming Tricks for Dynamic Ways & Means Simulations: Splitting Force Updates to Reduce Computational Work (2001) (0)
Molecular dynamics studies of polymerase X/DNA complexes in the presence of OxoG on the templating strand (2012) (0)
Effect of Single-Residue Mutations on CTCF Binding to DNA: Insights from Molecular Dynamics Simulations (2023) (0)
Faculty Opinions recommendation of An algorithmic game-theory approach for coarse-grain prediction of RNA 3D structure. (2013) (0)
Unraveling Genome Biophysics. (2017) (0)
Biomolecular Structure and Modeling: Problem and Application Perspective (2010) (0)
Cover Image, Volume 10, Issue 2 (2019) (0)
Development of a new computational approach for the prediction of nucleic acid structure by potential energy methods: I. Deoxyribose (1986) (0)
Faculty Opinions recommendation of Buffed energy landscapes: another solution to the kinetic paradoxes of protein folding. (2003) (0)
Conformational explorations into DNA polymerase X from African swine fever virus in the presence of oxoG lesions (2011) (0)
Faculty Opinions recommendation of Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids. (2002) (0)
MODERN LUNAR SOCIETY (2005) (0)
Methods for Macromolecular Modeling (M3): Assessment of Progress and Future Perspectives (2002) (0)
Faculty Opinions recommendation of Multiple conformational selection and induced fit events take place in allosteric propagation. (2014) (0)
Chromatin Structure Regulation by an Epigenetic Switch Tuning the Flexibility of the H1 C-Terminal Domain (2019) (0)
Structure of a binary complex of the R517A Pol lambda mutant (2008) (0)
Faculty Opinions recommendation of Combinatorial informatics in the post-genomics ERA. (2002) (0)
Faculty Opinions recommendation of Structures of dNTP intermediate states during DNA polymerase active site assembly. (2012) (0)
The Template Pattern (2007) (0)
Chromatin unfolding by epigenetic modifications explained by dramatic impairment of internucleosome interactions : a multiscale study (2017) (0)
Parallel Numerical Methods, Software Development and Applications (2013) (0)
A new pair of algorithms for potential energy minimization and molecular dynamics simulations (1989) (0)

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