References
- Kleywegt GJ, Harris MR, Zou JY, Taylor TC, Wahlby A, Jones TA. The Uppsala Electron-Density Server. Acta Crystallogr. D Biol. Crystallogr.60(12 Pt 1), 2240–2249 (2004).
- Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure15(9), 1040–1052 (2007).
- Poon BK, Chen X, Lu M et al. Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42aA crystallographic resolution. Proc. Natl Acad. Sci. USA104(19), 7869–7874 (2007).
- Case DA, Cheatham TE 3rd, Darden T et al. The Amber biomolecular simulation programs. J. Comput. Chem.26(16), 1668–1688 (2005).
- Hawkins PC, Warren GL, Skillman AG, Nicholls A. How to do an evaluation: pitfalls and traps. J. Comput. Aided Mol. Des.22(3–4), 179–190 (2008).
- Tirado-Rives J, Jorgensen WL. Contribution of conformer focusing to the uncertainty in predicting free energies for protein–ligand binding. J. Med. Chem.49(20), 5880–5884 (2006).
- Jorgensen WL, Ruiz-Caro J, Tirado-Rives J, Basavapathruni A, Anderson KS, Hamilton AD. Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase. Bioorg. Med. Chem. Lett.16(3), 663–667 (2006).
- Wang J, Deng Y, Roux B. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys. J.91(8), 2798–2814 (2006).
- Steuber H, Heine A, Klebe G. Structural and thermodynamic study on aldose reductase: nitro-substituted inhibitors with strong enthalpic binding contribution. J. Mol. Biol.368(3), 618–638 (2007).
- Gerlach C, Smolinski M, Steuber H et al. Thermodynamic inhibition profile of a cyclopentyl and a cyclohexyl derivative towards thrombin: the same but for different reasons. Angew. Chem. Int. Ed. Engl.46(44), 8511–8514 (2007).
- Feng BY, Simeonov A, Jadhav A et al. A high-throughput screen for aggregation-based inhibition in a large compound library. J. Med. Chem.50(10), 2385–2390 (2007).
- Babaoglu K, Simeonov A, Irwin JJ et al. Comprehensive mechanistic analysis of hits from high-throughput and docking screens against β-lactamase. J. Med. Chem.51(8), 2502–2511(2008).
- Kuntz ID, Chen K, Sharp KA, Kollman PA. The maximal affinity of ligands. Proc. Natl Acad. Sci. USA96(18), 9997–10002 (1999).
- Reynolds CH, Tounge BA, Bembenek SD. Ligand binding efficiency: trends, physical basis, and implications. J. Med. Chem.51(8), 2432–2438 (2008).
- Hajduk PJ. Fragment-based drug design: how big is too big? J. Med. Chem.49(24), 6972–6976 (2006).
- Hajduk PJ. Puzzling through fragment-based drug design. Nat. Chem. Biol.2(12), 658–659 (2006).
- Babaoglu K, Shoichet BK. Deconstructing fragment-based inhibitor discovery. Nat. Chem. Biol.2(12), 720–723 (2006).
- Hajduk PJ, Greer J. A decade of fragment-based drug design: strategic advances and lessons learned. Nat. Rev. Drug Discov.6(3), 211–219 (2007).
Website
- The Binding Database www.bindingdb.org/bind/index.jsp