Combined docking and molecular dynamics (MD) simulations are carried out for the rational design of affinity peptide ligand of tissue-type plasminogen activator (t-PA).
Combined docking and molecular dynamics simulations will be used to design small molecules that mimic the peptide-active site interactions [37].
The PECr model was then used as a starting point to generate the missing region of the cytosolic part of PTP-SL (aa147 253), by combined docking, ab-initio and homology modeling.
The combined docking model of Sk45 tertiary complex with integrin cytoplasmic tails is presented in Figure 5 and discussed below.
Gordon EA, Whisenant TC, Zeller M, Kaake RM, Gordon WM, Krotee P, et al. Combining docking site and phosphosite predictions to find new substrates: identification of smoothelin-like-2 (SMTNL2) as a c-Jun N-terminal kinase (JNK) substrate.
In summary, combining docking with pharmacophore searches as a post-processing filter allows the advantages of both methods to be fully exploited.
Combining docking studies with KRIPO and experimental data on complex III inhibition enabled us to explain the molecular details of statin binding to the predicted binding site.
Examples of these methods include IMPACTS [9], which combines docking with a fragment based reactivity approach, and a recently published approach [10] that makes use of a tethered docking methodology using GOLD [11] combined with a reactivity approach based on hydrogen bond order descriptors and a novel implementation of the average local ionisation energy.
We used a structure-based approach combining docking of FAK and p53 peptide interaction and molecular docking of small molecule compounds with functional testing, as described [ 33].
Therefore, with the crystal structure of human ATG4B established and the active site mapped, we performed in silico compound docking combined with cell-based assays to identify putative small molecule inhibitors of ATG4B and autophagy.
