AutoDock Version 4.2

More documents

Recommendations

Info

$Small-Angle X-ray Scattering SAXS vs. X-ray Diffraction SAXS vs. X ...$

(3) If you can’t find the answer to your problem, send your question to the AutoDock List(ADL) or the AutoDock Forum. There are many seasoned users of computational chemistrysoftware and some AutoDock users who may already know the answer to your question. You canfind out more about the ADL on the WWW at:http://mgldev.scripps.edu/mailman/listinfo/autodockThe Forum is available on the WWW at:http://mgl.scripps.edu/forum(4) If you have tried (1), (2) and (3), and you still cannot find an answer, send email togoodsell@scripps.edu for questions about AutoGrid or AutoDock; or to rhuey@scripps.edu, forquestions about AutoDockTools.Thanks for your understanding!E-mail addressesArthur J. Olson, Ph.D. olson@scripps.eduDavid S. Goodsell, Ph.D. goodsell@scripps.eduRuth Huey, Ph.D. rhuey@scripps.eduFax: + (858) 784-2860The Scripps Research Institute,Molecular Graphics Laboratory,Department of Molecular Biology, Mail Drop MB-5,10550 North Torrey Pines Road,La Jolla, CA 92037-1000, U.S.A.6
TheoryOverview of the Free Energy FunctionAutoDock 4.2 uses a semiempirical free energy force field to evaluate conformations duringdocking simulations. The force field was parameterized using a large number of protein-inhibitorcomplexes for which both structure and inhibition constants, or K i, are known.The force field evaluates binding in two steps. The ligand and protein start in an unboundconformation. In the first step, the intramolecular energetics are estimated for the transition fromthese unbound states to the conformation of the ligand and protein in the bound state. The secondstep then evaluates the intermolecular energetics of combining the ligand and protein in their boundconformation.The force field includes six pair-wise evaluations (V) and an estimate of the conformational entropylost upon binding (ΔS conf):ΔG = (V L−LboundL−L−V unbound) + (V P−PboundP−P−V unbound) + (V P−L P−Lbound−V unbound+ ΔS conf)€where L refers to the “ligand” and P refers to the “protein” in a ligand-protein dockingcalculation.Each of the pair-wise energetic terms includes evaluations for dispersion/repulsion, hydrogenbonding, electrostatics, and desolvation:⎛ AV = Wijvdw 12r − B ⎞⎛ij∑ ⎜ 6⎝ ijr⎟ + W hbondE(t) C ij12i, jij ⎠r − D ⎞ij∑ ⎜ 10⎝ ijr⎟ + W ∑ q iq jeleci, jij ⎠i, jε(r ij)r + W ∑( S V + S V ) e (−r ij 2 / 2σ 2 )sol i j j iiji, j€7
Page 5: Expanded Atom Types. Parameters hav
Page 9 and 10: AutoDock Potentials. Examples of th
Page 11 and 12: Care should be taken when the PDB f
Page 13 and 14: Edit>Delete: several options for de
Page 15 and 16: STEP 2: Running AutoGridAutoDock re
Page 17 and 18: STEP 3: Docking with AutoDockAutoDo
Page 19 and 20: “unbound_model_extended.” This
Page 21 and 22: STEP 4: Evaluating the Results of a
Page 23 and 24: Clusterings>Recluster: Reclusters d
Page 25 and 26: Sample PDBQT fileREMARK 4 active to
Page 27 and 28: AutoGrid Grid Parameter File: GPFEx
Page 29 and 30: Atomic Parameter FileFilename: AD4.
Page 31 and 32: Grid Map FileExtension: .mapThe fir
Page 33 and 34: AutoDock Docking Parameter File: DP
Page 35 and 36: Filename for the electrostatics gri
Page 37 and 38: falls within a disallowed zone, how
Page 39 and 40: is small enough to fit into the low
Page 41 and 42: [10]This is the number of preceding
Page 43 and 44: do_global_only [50]This keyword ins
Page 45 and 46: Ring closure parameters. Comparison
Page 47 and 48: implicit limit of the docking compl
Page 49: Appendix III: AutoDock ReferencesAu

AutoDock Version 4.2

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?