Tamar Schlick

According to our database, Tamar Schlick authored at least 36 papers between 1991 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2021

Publisher Correction: Biomolecular modeling thrives in the age of technology.

Tamar Schlick, Stephanie Portillo-Ledesma

Nat. Comput. Sci., 2021

Biomolecular modeling thrives in the age of technology.

Tamar Schlick, Stephanie Portillo-Ledesma

Nat. Comput. Sci., 2021

2020

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

Grace Meng, Marva Tariq, Swati Jain, Shereef Elmetwaly, Tamar Schlick

Bioinform., 2020

2019

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

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

J. Comput. Chem., 2019

Graph-Theoretic Partitioning of RNAs and Classification of Pseudoknots.

Louis Petingi, Tamar Schlick

Proceedings of the Algorithms for Computational Biology - 6th International Conference, 2019

2016

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

Lei Hua, Yang Song, Namhee Kim, Christian Laing, Jason T. L. Wang, Tamar Schlick

CoRR, 2016

2015

Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.

Bret D. Freudenthal, William A. Beard, Lalith E. Perera, David D. Shock, Taejin Kim, Tamar Schlick, Samuel H. Wilson

Nat., 2015

2013

"Gate-keeper" Residues and Active-Site Rearrangements in DNA Polymerase μ Help Discriminate Non-cognate Nucleotides.

Yunlang Li, Tamar Schlick

PLoS Comput. Biol., 2013

2012

Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function.

Giulio Quarta, Ken Sin, Tamar Schlick

PLoS Comput. Biol., 2012

2011

RAG: An Update to the RNA-As-Graphs Resource.

Joseph A. Izzo, Namhee Kim, Shereef Elmetwaly, Tamar Schlick

BMC Bioinform., 2011

2007

RAGPOOLS: RNA-As-Graph-Pools - a web server for assisting the design of structured RNA pools for <i>in vitro</i> selection.

Namhee Kim, Jin Sup Shin, Shereef Elmetwaly, Hin Hark Gan, Tamar Schlick

Bioinform., 2007

2006

Special Section On Multiscale Modeling In Biology.

Tamar Schlick, Ken A. Dill

Multiscale Model. Simul., 2006

2004

RAG: RNA-As-Graphs web resource.

Daniela Fera, Namhee Kim, Nahum Shiffeldrim, Julie Zorn, Uri Laserson, Hin Hark Gan, Tamar Schlick

BMC Bioinform., 2004

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

Hin Hark Gan, Daniela Fera, Julie Zorn, Nahum Shiffeldrim, Michael Tang, Uri Laserson, Namhee Kim, Tamar Schlick

Bioinform., 2004

Searching for 2D RNA geometries in bacterial genomes.

Uri Laserson, Hin Hark Gan, Tamar Schlick

Proceedings of the 20th ACM Symposium on Computational Geometry, 2004

2003

Multiplicative Operator Splittings in Nonlinear Diffusion: From Spatial Splitting to Multiple Timesteps.

Danny Barash, Tamar Schlick, Moshe Israeli, Ron Kimmel

J. Math. Imaging Vis., 2003

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

Qing Zhang, Daniel A. Beard, Tamar Schlick

J. Comput. Chem., 2003

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

Danny Barash, Linjing Yang, Xiaoliang Qian, Tamar Schlick

J. Comput. Chem., 2003

2002

A More Lenient Stopping Rule for Line Search Algorithms.

Dexuan Xie, Tamar Schlick

Optim. Methods Softw., 2002

2001

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

Xiaoliang Qian, Daniel Strahs, Tamar Schlick

J. Comput. Chem., 2001

2000

An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization.

Dexuan Xie, Alexander Tropsha, Tamar Schlick

J. Chem. Inf. Comput. Sci., 2000

Computational challenges in simulating large DNA over long times.

Tamar Schlick, Daniel A. Beard, Jing Huang, Daniel Strahs, Xiaoliang Qian

Comput. Sci. Eng., 2000

1999

Remark on Algorithm 702 - the updated truncated Newton minimization package.

Dexuan Xie, Tamar Schlick

ACM Trans. Math. Softw., 1999

Efficient Implementation of the Truncated-Newton Algorithm for Large-Scale Chemistry Applications.

Dexuan Xie, Tamar Schlick

SIAM J. Optim., 1999

Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations.

Tamar Schlick

Proceedings of the Computational Molecular Dynamics: Challenges, Methods, Ideas, 1999

1998

An adaptive multigrid technique for evaluating long-range forces in biomolecular simulations.

Leonid Y. Zaslavsky, Tamar Schlick

Appl. Math. Comput., 1998

1997

A Family of Symplectic Integrators: Stability, Accuracy, and Molecular Dynamics Applications.

Robert D. Skeel, Guihua Zhang, Tamar Schlick

SIAM J. Sci. Comput., 1997

1994

Remark on Algorithm 566.

Victoria Z. Averbukh, Samuel Figueroa, Tamar Schlick

ACM Trans. Math. Softw., 1994

A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications.

Philippe Derreumaux, Guihua Zhang, Tamar Schlick, Bernard R. Brooks

J. Comput. Chem., 1994

1993

Modified Cholesky Factorizations for Sparse Preconditioners.

Tamar Schlick

SIAM J. Sci. Comput., 1993

Numerical Experience with Limited-Memory Quasi-Newton and Truncated Newton Methods.

X. Zou, Ionel Michael Navon, M. Berger, Paul Kang-Hoh Phua, Tamar Schlick, François-Xavier Le Dimet

SIAM J. Optim., 1993

LIN: A new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal mode techniques.

Guihua Zhang, Tamar Schlick

J. Comput. Chem., 1993

1992

Algorithm 702: TNPACK-a truncated Newton minimization package for large-scale problems: I. Algorithm and usage.

Tamar Schlick, Aaron L. Fogelson

ACM Trans. Math. Softw., 1992

TNPACK - a truncated Newton minimization package for large-scale problems: II. Implementation examples.

Tamar Schlick, Aaron L. Fogelson

ACM Trans. Math. Softw., 1992

TNPACK - A truncated Newton minimization package for large-scale problems: I. Algorithm and usage.

Tamar Schlick, Aaron L. Fogelson

ACM Trans. Math. Softw., 1992

1991

New Approaches to Potential Energy Minimization and Molecular Dynamics Algorithms.

Tamar Schlick

Comput. Chem., 1991