| ## RNAstructure Installation and Overview Contributors | ### Contents ### Index
Stas Bellaousov wrote ShapeKnots, updated NAPSS, and contributed to ProbKnot and orega. He helped determine the ShapeKnots energy function and optimal parameters. Jonathan Chen helped design the NAPSS program. Clarence Yu Cheng implemented experimentally-determined pairing bonuses and updated DMS mapping in ShapeKnots. Pablo Cordero added the ability of efn2 to use SHAPE data and the ability to apply pairing energy restraints in Fold. He added a knowledge-based method for determining stacking restraints from chemical mapping data. Rhiju Das added the ability of efn2 to use SHAPE data and the ability to apply pairing energy restraints in Fold. He added a knowledge-based method for determining stacking restraints from chemical mapping data. He implemented experimentally-determined pairing bonuses and updated DMS mapping in ShapeKnots. Katie Deigan contributed to the methods for using SHAPE data to restrain secondary structure prediction. Laura DiChiacchio wrote the DuplexFold and AccessFold programs. Yinghan Fu wrote Multifind and revised Dynalign to make Dynalign II. Jason Gloor wrote the first implementation of MaxExpect. Christine Hajdin contributed to ShapeKnots. She also contributed to the design of CircleCompare. Arif Harmanci wrote PARTS, TurboFold, and the pairwise alignment HMM. Jim Hart wrote NAPSS. Liang Huang and his group developed ThreshKnot. Wayne Huggins contributed to ShapeKnots. Joshua Keegan wrote the first configuration file implementation, used by Dynalign, PARTS, TurboFold, and Multilign. Mohammad Kayedkhordeh incorporated the ensemble defect calculator and the linearly scaling multibranch and exterior loop codes. He also developed orega (the genetic algorithm for evolving sequences). John Lu extended OligoWalk, wrote the OligoWalk command line interface, added the O(N^3) code for predicting internal loops of any size in free energy minimization and the partition function, and wrote the OligoWalk web server. Jacob Mainzer wrote the extended_double type and added single-stranded SHAPE constraints to free energy minimization. David Mathews wrote many of the original components (free energy minimization, efn2, partition, Dynalign), the Windows GUI (now deprecated), and the first components of the class library. He also worked on the revision that enables extended folding alphabets. He wrote the design program. Anthony Mustoe contributed to the handling of restraints in ShapeKnots. He also updated the use of DMS maping data in Fold. Jessica Reuter wrote the JAVA GUI, the Makefile system, CircleCompare and most of the command line interfaces. Michael Sloma write the CycleFold program. He also wrote many of the SMP versions of the programs. Michael also wrote the fold-cuda and ProbScan programs, the python interface to RNAstructure, and the interface to phmm. He also adapted the draw program to annotate loop and helix probabilities. He also contributed to the implementation of the extended alphabet. Michale wrote the initial code for orega (the genetic algorithm for evolving sequences). Aleksandar Spasic wrote the Rsample program. Harry Stern wrote partition-cuda. Zhen Tan revised TurbFold to make TurboFold II. He also wrote TurboHomology. Siqi Tian implemented experimentally-determined pairing bonuses and updated DMS mapping in ShapeKnots. Paul Tymann, Glenn Katzen, Chris Connett, and Andrew Yohn, Computer Science, Rochester Institute of Technology, contributed changes that accelerated Dynalign and also wrote the SMP version of Dynalign. Max Ward-Graham contributed the energy calculator class. He also removed bugs in Fold. Richard Watson wrote the drawing program. He modernized the Makefile and testing systems. He wrote the tests of the JAVA GUI. He also wrote the interface for Design and the GUI interfaces for Design and ProbKnot. He also contributed to the extended alphabet code. Kevin Weeks contributed to way Fold uses SHAPE data to restrain secondary structure prediction. He also conceived of the CircleCompare program. He helped to determine the energy function and optimal parameters for ShapeKnots. Zhenjiang Xu wrote the Multilign algorithm. He Zhang contributed to ThreshKnot. Liang Zhang developed ThreshKnot. Xiaoju Zhang developed the new datatable format for expanded alphabets and wrote the new datatable reading functions. Jeff Zuber wrote code to calculate multibranch and exterior loop free energies with linear scaling. He revised the partition function to store arrays in the logarithmic space. He also added error estimation to efn2.