Tamar Schlick

37 papers Journal 34Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors.
PLoS Comput. Biol.
Rui Wang, Tamar Schlick
2021 J jnl
Biomolecular modeling thrives in the age of technology.
Nat. Comput. Sci.
Tamar Schlick, Stephanie Portillo-Ledesma
2021 J jnl
Publisher Correction: Biomolecular modeling thrives in the age of technology.
Nat. Comput. Sci.
Tamar Schlick, Stephanie Portillo-Ledesma
2020 J jnl
RAG-Web: RNA structure prediction/design using RNA-As-Graphs.
Bioinform.
Grace Meng, Marva Tariq, Swati Jain, Shereef Elmetwaly, Tamar Schlick
2019 — conf
Graph-Theoretic Partitioning of RNAs and Classification of Pseudoknots.
AlCoB
Louis Petingi, Tamar Schlick
2019 J jnl
Scaling molecular dynamics beyond 100, 000 processor cores for large-scale biophysical simulations.
J. Comput. Chem.
Jaewoon Jung, Wataru Nishima, Marcus Daniels, Gavin Bascom, Chigusa Kobayashi, Adetokunbo Adedoyin, Michael E. Wall, Anna Lappala, Dominic Phillips, William Fischer, Chang-Shung Tung, Tamar Schlick, Yuji Sugita, Karissa Y. Sanbonmatsu
2016 J jnl
CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking.
CoRR
Lei Hua, Yang Song, Namhee Kim, Christian Laing, Jason T. L. Wang, Tamar Schlick
2015 J jnl
Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.
Nat.
Bret D. Freudenthal, William A. Beard, Lalith E. Perera, David D. Shock, Taejin Kim, Tamar Schlick, Samuel H. Wilson
2013 J jnl
"Gate-keeper" Residues and Active-Site Rearrangements in DNA Polymerase μ Help Discriminate Non-cognate Nucleotides.
PLoS Comput. Biol.
Yunlang Li, Tamar Schlick
2012 J jnl
Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function.
PLoS Comput. Biol.
Giulio Quarta, Ken Sin, Tamar Schlick
2011 J jnl
RAG: An Update to the RNA-As-Graphs Resource.
BMC Bioinform.
Joseph A. Izzo, Namhee Kim, Shereef Elmetwaly, Tamar Schlick
2007 J jnl
RAGPOOLS: RNA-As-Graph-Pools - a web server for assisting the design of structured RNA pools for
Bioinform.
Namhee Kim, Jin Sup Shin, Shereef Elmetwaly, Hin Hark Gan, Tamar Schlick
2006 J jnl
Special Section On Multiscale Modeling In Biology.
Multiscale Model. Simul.
Tamar Schlick, Ken A. Dill
2004 J jnl
RAG: RNA-As-Graphs database-concepts, analysis, features.
Bioinform.
Hin Hark Gan, Daniela Fera, Julie Zorn, Nahum Shiffeldrim, Michael Tang, Uri Laserson, Namhee Kim, Tamar Schlick
2004 J jnl
RAG: RNA-As-Graphs web resource.
BMC Bioinform.
Daniela Fera, Namhee Kim, Nahum Shiffeldrim, Julie Zorn, Uri Laserson, Hin Hark Gan, Tamar Schlick
2004 — conf
Searching for 2D RNA geometries in bacterial genomes.
SCG
Uri Laserson, Hin Hark Gan, Tamar Schlick
2003 J jnl
Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm.
J. Comput. Chem.
Qing Zhang, Daniel A. Beard, Tamar Schlick
2003 J jnl
Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms.
J. Comput. Chem.
Danny Barash, Linjing Yang, Xiaoliang Qian, Tamar Schlick
2003 J jnl
Multiplicative Operator Splittings in Nonlinear Diffusion: From Spatial Splitting to Multiple Timesteps.
J. Math. Imaging Vis.
Danny Barash, Tamar Schlick, Moshe Israeli, Ron Kimmel
2002 J jnl
A More Lenient Stopping Rule for Line Search Algorithms.
Optim. Methods Softw.
Dexuan Xie, Tamar Schlick
2001 J jnl
A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID).
J. Comput. Chem.
Xiaoliang Qian, Daniel Strahs, Tamar Schlick
2000 J jnl
An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization.
J. Chem. Inf. Comput. Sci.
Dexuan Xie, Alexander Tropsha, Tamar Schlick
2000 J jnl
Computational challenges in simulating large DNA over long times.
Comput. Sci. Eng.
Tamar Schlick, Daniel A. Beard, Jing Huang, Daniel Strahs, Xiaoliang Qian
1999 J jnl
Efficient Implementation of the Truncated-Newton Algorithm for Large-Scale Chemistry Applications.
SIAM J. Optim.
Dexuan Xie, Tamar Schlick
1999 J jnl
Remark on Algorithm 702 - the updated truncated Newton minimization package.
ACM Trans. Math. Softw.
Dexuan Xie, Tamar Schlick
1999 — ch.
Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations.
Computational Molecular Dynamics
Tamar Schlick
1998 J jnl
An adaptive multigrid technique for evaluating long-range forces in biomolecular simulations.
Appl. Math. Comput.
Leonid Y. Zaslavsky, Tamar Schlick
1997 J jnl
A Family of Symplectic Integrators: Stability, Accuracy, and Molecular Dynamics Applications.
SIAM J. Sci. Comput.
Robert D. Skeel, Guihua Zhang, Tamar Schlick
1994 J jnl
A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications.
J. Comput. Chem.
Philippe Derreumaux, Guihua Zhang, Tamar Schlick, Bernard R. Brooks
1994 J jnl
Remark on Algorithm 566.
ACM Trans. Math. Softw.
Victoria Z. Averbukh, Samuel Figueroa, Tamar Schlick
1993 J jnl
LIN: A new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal mode techniques.
J. Comput. Chem.
Guihua Zhang, Tamar Schlick
1993 J jnl
Modified Cholesky Factorizations for Sparse Preconditioners.
SIAM J. Sci. Comput.
Tamar Schlick
1993 J jnl
Numerical Experience with Limited-Memory Quasi-Newton and Truncated Newton Methods.
SIAM J. Optim.
Xiaolei Zou, Ionel Michael Navon, M. Berger, Paul Kang-Hoh Phua, Tamar Schlick, François-Xavier Le Dimet
1992 J jnl
Algorithm 702: TNPACK-a truncated Newton minimization package for large-scale problems: I. Algorithm and usage.
ACM Trans. Math. Softw.
Tamar Schlick, Aaron L. Fogelson
1992 J jnl
TNPACK - A truncated Newton minimization package for large-scale problems: I. Algorithm and usage.
ACM Trans. Math. Softw.
Tamar Schlick, Aaron L. Fogelson
1992 J jnl
TNPACK - a truncated Newton minimization package for large-scale problems: II. Implementation examples.
ACM Trans. Math. Softw.
Tamar Schlick, Aaron L. Fogelson
1991 J jnl
New Approaches to Potential Energy Minimization and Molecular Dynamics Algorithms.
Comput. Chem.
Tamar Schlick