- 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
- 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
- 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).
- 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).
- 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).
- Main features include representing RNA secondary structure as three-dimensional tree graphs and sampling different graph topologies; fragment assembly for RNA graphs (F-RAG) to generate 3D atomic models of RNA for graphs, and design of sequences to fold onto RNA-like tree graph topologies