How good is automated protein docking?

Abstract

The protein docking server ClusPro has been participating in CAPRI since its introduction in 2004. This paper evaluates the performance of ClusPro 2.0 for targets 46–58 in rounds 22–27 of CAPRI. The analysis leads to a number of important observations. First, ClusPro reliably yields acceptable or medium accuracy models for targets of moderate difficulty that have also been successfully predicted by other groups, and fails only for targets that have few acceptable models submitted. Second, the quality of automated docking by ClusPro is very close to that of the best human predictor groups, including our own submissions. This is very important, because servers have to submit results within 48 hours and the predictions should be reproducible, whereas human predictors have several weeks and can use any type of information. Third, while we refined the ClusPro results for manual submission by running computationally costly Monte Carlo minimization simulations, we observed significant improvement in accuracy only for two of the six complexes correctly predicted by ClusPro. Fourth, new developments, not seen in previous rounds of CAPRI, are that the top ranked model provided by ClusPro was acceptable or better quality for all these six targets, and that the top ranked model was also the highest quality for five of the six, confirming that ranking models based on cluster size can reliably identify the best near-native conformations.

Interference of HCV replication by cell penetrable human monoclonal scFv specific to NS5B polymerase

“…The NS5BD55 and SLD3 RNA (5 0 GGGCUUGCAU AGCAAGUCUG AGACC 3 0 ) 45 were used as a source of active polymerase and as RNA template, respectively. A polymerase reaction mixture (80 ml containing 300 nM of NS5BD55, 20 mM sodium glutamate pH 8.2, 4 mM MgCl 2 , 12.5 mM DTT, 0.5% (v/v) Triton £ -100, 2 mM MnCl 2 , 40 units RNase inhibitor, and 200 mM each of ATP, UTP, GTP, and biotinylated-CTP) was added to the SLD3 RNA coated well and incubated at 37 C for 2 h. In the presence of active RdRp, newly synthesized RNA containing biotinylated-CTP was detectable by adding streptavidin-HRP conjugate (Southern Biotech, USA) and ABTS substrate (KPL, USA), respectively. The OD 405nm of the content of each well was determined.…”

“…The scFv-14 and -34 (5 mg in 50 ml PBS) were incubated separately with various amounts of the mimotopic phages (M14, M34/1, M34/2 and M34/3), M34-1, M34-2 and M34-3 mixture and synthetic peptides identical to the NS5B epitopes matched with the M14, M34/1, M34/2, and M34/3 phage mimotopes, i.e., LRKLGCPPLRAW (P14), PISPLSNSLLRHHNLVY (P34-1), GLSAFTLHSYSP (P34-2), and PPLRAWRHRARA (P34-3) and mixture of the peptides at 37 C for 1 h. Background and negative inhibition controls (maximum binding, 100%) consisted of the scFvs mixed with control phage/peptide and buffer only. Thereafter, all reaction mixtures were added appropriately to ELISA wells pre-coated with the NS5BD55.…”

“…The JFH-1 RNA transfected cells that had been treated with the PEN-scFvs, irrelevant PEN-scFv, PEG-IFNCRBV and medium alone for 5 d and their spent culture fluids were collected for the foci assay. After collecting the culture fluid, the infected cells in each well were rinsed with sterile PBS, fixed with absolute methanol and blocked with 10% BSA before incubating with mouse immune serum to HCV C protein (prepared by injecting recombinant C protein of HCV genotype 3a mixed with alum intramuscularly into BALB/c mice; two booster doses were given to the primed mice at two week intervals and the mice were bled at day 7 post-last booster for immune serum collection) at 37 C for 1 h in order to locate the infected cells. After rinsing, the cells were added with goat anti-mouse immunoglobulin-AP conjugate and BCIP/NBT substrate, respectively, with washing between the steps.…”

“…[31][32][33][34][35][36][37][38] The NS5B of HCV genotype 3a's linear sequence (accession number NP751928) was used in the alignment with the scFv mimotope sequences for tentative epitope identification and the 3D structure of PDB 1C2P was used in the molecular docking with the scFv 3D structures. Although the principles of the two methods are different (the phage mimotope search was based on the linear sequences of both the mimotopes and the NS5B while the computerized molecular docking encompassed 3D structures and conformational epitopes), the results were, more or less, conformed.…”

Integrative computational modeling of protein interactions

“…All the listed methods offer the possibility to integrate data into their algorithms, although they differ in the stage at which the data can be incorporated and in their implementation. FFT-based approaches (ClusPro [66], pyDock [21], GRAMM-X [67], ZDOCK [61] and HEX [26]) evaluate very large numbers of interaction modes and implement the data as a scoring bias intermolecular axis defined by a pair of residues, one on each interacting monomer. The angular range of the search can also be defined.…”