Ben Knowles

Software

• Monte carlo calculation of molecular excluded volumes
• Random polymer generation
• Output parser for the Surface Racer program
• Small-molecule bond dihedral randomizer (for generating ensembles of random conformers) and other simple functions for manipulating small molecule structures in Matlab
• autoμsic: A Matlab library for computer-assisted composition of music
  

Papers

1. Separating chemical and excluded volume interactions of polyethylene glycols with native proteins: Comparison with PEG effects on DNA helix formation.
   Irina A. Shkel, Ben Knowles, and M. Thomas Record, Jr.
   Biopolymers | Pubmed | PDF
2. Chemical Interactions of Polyethylene Glycols (PEGs) and Glycerol with Protein Functional Groups: Applications to Effects of PEG and Glycerol on Protein Processes
   DB Knowles, Irina A Shkel, Noel M Phan, Matt Sternke, Emily Lingeman, Xian Cheng, Lixue Cheng, Kevin O'Connor, and M. Thomas Record, Jr.
   Biochemistry | Pubmed | PDF | SI
3. Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability
   D. B. Knowles, Andrew S. LaCroix, Nickolas F. Deines, Irina Shkel, and M. Thomas Record, Jr.
   PNAS | Pubmed | PDF
4. Characterization of Solanum tuberosum Multicystatin and Its Structural comparison with Other Cystatins
   Mark S. Nissen, G.N. Mohan Kumar, Buhyun Youn, D.Benjamin Knowles, Ka Sum Lam, W. Jordan Ballinger, N. Richard Knowles, and ChulHee Kan
   The Plant Cell | Pubmed | PDF
5. Crystal structures of NADH:FMN oxidoreductase (EmoB) at different stages of catalysis
   Nissen MS, Youn B, Knowles DB, Ballinger JW, Jun SY, Belchik SM, Xun L, Kang C.
   JBC | Pubmed | PDF