Tamar Schlick

According to our database1, Tamar Schlick authored at least 34 papers between 1991 and 2020.

Collaborative distances:

Timeline

Legend:

Book 
In proceedings 
Article 
PhD thesis 
Other 

Links

Online presence:

On csauthors.net:

Bibliography

2020
RAG-Web: RNA structure prediction/design using RNA-As-Graphs.
Bioinform., 2020

2019
Scaling molecular dynamics beyond 100, 000 processor cores for large-scale biophysical simulations.
J. Comput. Chem., 2019

Graph-Theoretic Partitioning of RNAs and Classification of Pseudoknots.
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.
CoRR, 2016

2015
Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.
Nat., 2015

2013
"Gate-keeper" Residues and Active-Site Rearrangements in DNA Polymerase μ Help Discriminate Non-cognate Nucleotides.
PLoS Comput. Biol., 2013

2012
Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function.
PLoS Comput. Biol., 2012

2011
RAG: An Update to the RNA-As-Graphs Resource.
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.
Bioinform., 2007

2006
Special Section On Multiscale Modeling In Biology.
Multiscale Model. Simul., 2006

2004
RAG: RNA-As-Graphs web resource.
BMC Bioinform., 2004

RAG: RNA-As-Graphs database-concepts, analysis, features.
Bioinform., 2004

Searching for 2D RNA geometries in bacterial genomes.
Proceedings of the 20th ACM Symposium on Computational Geometry, 2004

2003
Multiplicative Operator Splittings in Nonlinear Diffusion: From Spatial Splitting to Multiple Timesteps.
J. Math. Imaging Vis., 2003

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm.
J. Comput. Chem., 2003

Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms.
J. Comput. Chem., 2003

2002
A More Lenient Stopping Rule for Line Search Algorithms.
Optim. Methods Softw., 2002

2001
A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID).
J. Comput. Chem., 2001

2000
An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization.
J. Chem. Inf. Comput. Sci., 2000

Computational challenges in simulating large DNA over long times.
Comput. Sci. Eng., 2000

1999
Remark on Algorithm 702 - the updated truncated Newton minimization package.
ACM Trans. Math. Softw., 1999

Efficient Implementation of the Truncated-Newton Algorithm for Large-Scale Chemistry Applications.
SIAM J. Optim., 1999

Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations.
Proceedings of the Computational Molecular Dynamics: Challenges, Methods, Ideas, 1999

1998
An adaptive multigrid technique for evaluating long-range forces in biomolecular simulations.
Appl. Math. Comput., 1998

1997
A Family of Symplectic Integrators: Stability, Accuracy, and Molecular Dynamics Applications.
SIAM J. Sci. Comput., 1997

1994
Remark on Algorithm 566.
ACM Trans. Math. Softw., 1994

A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications.
J. Comput. Chem., 1994

1993
Modified Cholesky Factorizations for Sparse Preconditioners.
SIAM J. Sci. Comput., 1993

Numerical Experience with Limited-Memory Quasi-Newton and Truncated Newton Methods.
SIAM J. Optim., 1993

LIN: A new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal mode techniques.
J. Comput. Chem., 1993

1992
Algorithm 702: TNPACK-a truncated Newton minimization package for large-scale problems: I. Algorithm and usage.
ACM Trans. Math. Softw., 1992

TNPACK - a truncated Newton minimization package for large-scale problems: II. Implementation examples.
ACM Trans. Math. Softw., 1992

TNPACK - A truncated Newton minimization package for large-scale problems: I. Algorithm and usage.
ACM Trans. Math. Softw., 1992

1991
New Approaches to Potential Energy Minimization and Molecular Dynamics Algorithms.
Comput. Chem., 1991


  Loading...