CADD References

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References and Citations

CADD Pipeline Related Publications

  1. Ren J, Williams N, Clementi L, Krishnan S and Li WW: Opal web services for biomedical applications. Nucleic Acids Res 38: W724-31, 2010.
  2. Amaro RE and Li WW: Emerging methods for ensemble-based virtual screening. Curr Top Med Chem 10: 3-13, 2010.
  3. Durrant, J. D.; McCammon, J. A., Computer-aided drug-discovery techniques that account for receptor flexibility. Curr Opin Pharmacol, Computer-aided drug-discovery techniques that account for receptor flexibility.

Component Software References

  1. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K., Scalable molecular dynamics with NAMD. J Comput Chem 2005, 26, (16), 1781-802, Scalable molecular dynamics with NAMD.
  2. Roberts, E.; Eargle, J.; Wright, D.; Luthey-Schulten, Z., MultiSeq: unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics 2006, 7, 382, MultiSeq: unifying sequence and structure data for evolutionary analysis.
  3. D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation programs. J. Computat. Chem. 26, 1668-1688 (2005).
  4. Yi Wang, Chris B. Harrison, Klaus Schulten, and J. Andrew McCammon. Implementation of accelerated molecular dynamics in NAMD. Computational Science & Discovery, 4:015002, 2011.

Relaxed Complex Scheme

  1. Lin, J. H.; Perryman, A. L.; Schames, J. R.; McCammon, J. A., The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 2003, 68, (1), 47-62, T0001. *
  2. Amaro, R. E.; Baron, R.; McCammon, J. A., An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des 2008, 22, (9), 693-705.


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