Software

 

- A program for calculating the curvature of nucleic acid.

- The Truncated-Newton optimization package.

- Peroidic Boundary Condition Setup (April 1999 version).

- Discrete Surface Charge Optimization

- Aims to engineer structured pools and examine pool properties for in vitro selection of RNAs and related problems

  1. N. Kim, J.S. Shin, S. Elmetwaly, H.H. Gan and T. Schlick, "RAGPOOLS: RNA-As-Graph-Pools A Web Server for Assisting the Design of Structured RNA Pools for In Vitro Selection", Bioinformatics, 23(21):2959-2960, doi:10.1093/bioinformatics/btm439 (2007)

- Aims to predict coaxial stacking and topologies for three and four-way junctions

  1. Namhee Kim, Christian Laing, Shereef Elmetwaly, Segun Jung, Jeremy Curuksu, and Tamar Schlick, "Graph-based sampling for approximating global helical topologies of RNA", PNAS, 111(11):4079-84 (2014).
  2. Christian Laing, Segun Jung, Namhee Kim, Shereef Elmetwaly, Mai Zahran, and Tamar Schlick, "Predicting Helical Topologies in RNA Junctions as Tree Graphs", PLoS ONE, 8(8): e71947, DOI:10.1371/journal.pone.0071947 (2013).
  3. Christian Laing, Dongrong Wen, Jason T. L. Wang and Tamar Schlick, "Predicting coaxial helical stacking in RNA junctions", Nucleic Acids Research, 40(2): 487-498, doi:10.1093/nar/gkr629 (2011).