Software (Machine learning, Analysis and Methods)

Codes are deposited into Yingling group public repository on GitHub


All-Atom Simulation Method for Zeeman Alignment and Dipolar Assembly of Magnetic Nanoparticles

Akhlak U. Mahmood and Yaroslava G. Yingling
ACS Journal of Chemical Theory and Computations (2022) DOI: 10.1021/acs.jctc.1c01253

An Implicit Solvent Ionic Strength (ISIS) Method to Model Polyelectrolyte Systems with Dissipative Particle Dynamics
N. K. Li, W. H. Fuss, Y. G. Yingling
Macromolecular Theory and Simulations 24 (2015) 7-12.

Coarse-Grained Model of the Interaction of Light with Polymeric Material: Onset of Ablation
Y. G. Yingling, B. J. Garrison
Journal of Physical Chemistry B 109 (2005) 16482-16489

Coarse Grained Chemical Reaction Model
Y. G. Yingling and B. J. Garrison
J. Phys. Chem. B 108 (2004) 1815

Predicted 3D structures

In silico structure prediction of full-length cotton cellulose synthase protein (GhCESA1) and its hierarchical complexes, Abhishek Singh, Albert L. Kwansa, Ho Shin Kim, Justin T. Williams, Hui Yang, Nan K. Li, James D. Kubicki, Alison W. Roberts, Candace H. Haigler, Yaroslava G. Yingling
Cellulose 27 (2020) 5597-5616 DOI: 10.1007/s10570-020-03194-7

Prediction of the structures of the plant-specific regions of vascular plant cellulose synthases and correlated functional analysis, Latsavongsakda Sethaphong, Jonathan K. Davis, Erin Slabaugh, Abhishek Singh, Candace H. Haigler, Yaroslava G. Yingling
Cellulose 23 (2016) 145-161 DOI: 10.1007/s10570-015-0789-6

Na+ Dependent Anion Transport by a Barley Efflux Protein Revealed through an Integrative Platform, Yagnesh Nagarajan, Jay Rongala, Sukanya Luang, Abhishek Singh, Nadim Shadiac, Julie Hayes, Tim Sutton, Matthew Gilliham, Stephen Tyerman, Gordon McPhee, Nicolas H. Voelcker, Hayden D. T. Mertens, Nigel Kirby, Jung-Goo Lee, Yaroslava G. Yingling, Maria Hrmova
Plant Cell 28 (2016) 202-218 DOI: 10.1105/tpc.15.00625

Cellulose synthase interactive 1 is required for a fast recycling of cellulose synthase complexes to the plasma membrane in Arabidopsis,  Lei Lei, Abhishek Singh, Logan Bashline, Shundai Li, Yaroslava G. Yingling, and Ying Gu
Plant Cell (2015) DOI: 10.1105/tpc.15.00442


RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
E.Bindewald, R. Hayes, Y. G. Yingling, W. Kasprzak, B. A. Shapiro
Nucleic Acids Res. 36 (2008) D392-D397


  1. K. Clendennen, Y. G. Yingling, H. Kim, (2018), CALB Variants, US010035995 B2 WO2017100240 A1. The invention relates to amino acid sequence variants of a lipase with improved activity for catalyzing synthesis reactions and methods of preparing the variants. The methods include predicting amino acid sites for change based on computational models of the protein structure in non-aqueous conditions, and expressing the protein in a prokaryotic host for subsequent purification and use. The enzyme sequence variants described have a three to nine-fold improvement in synthesis activity over the parent protein sequence.
  2. A. Shapiro, Y. G. Yingling, E. Bindewald, W. Kasprzak, L. Jaeger, I. Severcan, C. Geary, K. Afonin (2010), RNA Nanoparticles and methods of use, WO2010148085-A1, US 20120263648 A1. The presently-disclosed subject matter relates to an artificial RNA nanostructure and method of use thereof. In particular, the presently-disclosed subject matter relates to RNA nanoparticles and RNA dendrimers, and methods of disease diagnosis and treatments using the RNA nanostructure and RNA dendrimers.
  3. G. Yingling, B. A. Shapiro (2007), RNA nanoparticles and nanotubes. EP2035043-A2; AU2007300734-A1; CA2654174-A1; US2010016409-A1. The instant invention provides polyvalent RNA nanoparticles comprising RNA motifs as building blocks that can form RNA nanotubes. The polyvalent RNA nanoparticles are suitable for therapeutic or diagnostic use in a number of diseases or disorders.