AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

Morris, Garrett M.; Huey, Ruth; Lindstrom, William M.; Sanner, Michel F.; Belew, Richard K.; Goodsell, David S.; Olson, Arthur J.

doi:10.1002/jcc.21256

Cited by 18,622 publications

(13,864 citation statements)

References 18 publications

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“…For BD with AutoDock4 and EADock the protein molecules were equipped with H-atoms using AutoDock Tools. 18 The ligand molecules (Table II) including co-factors and solvent additives were equipped with H-atoms and energyminimized using Mopac 6 29 with a PM3 Hamiltonian and eigenvector following routine for energy minimization (except of HEME for where the crystal structure was used). In all cases, the force constant matrices were positive definite.…”

Section: Preparation Of Protein and Ligand Moleculesmentioning

confidence: 99%

Toward prediction of functional protein pockets using blind docking and pocket search algorithms

Hetényi

Spoel

2011

Protein Science

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Location of functional binding pockets of bioactive ligands on protein molecules is essential in structural genomics and drug design projects. If the experimental determination of ligand-protein complex structures is complicated, blind docking (BD) and pocket search (PS) calculations can help in the prediction of atomic resolution binding mode and the location of the pocket of a ligand on the entire protein surface. Whereas the number of successful predictions by these methods is increasing even for the complicated cases of exosites or allosteric binding sites, their reliability has not been fully established. For a critical assessment of reliability, we use a set of ligand-protein complexes, which were found to be problematic in previous studies. The robustness of BD and PS methods is addressed in terms of success of the selection of truly functional pockets from among the many putative ones identified on the surfaces of ligand-bound and ligand-free (holo and apo) protein forms. Issues related to BD such as effect of hydration, existence of multiple pockets, and competition of subsidiary ligands are considered. Practical cases of PS are discussed, categorized and strategies are recommended for handling the different situations. PS can be used in conjunction with BD, as we find that a consensus approach combining the techniques improves predictive power.

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Section: Preparation Of Protein and Ligand Moleculesmentioning

confidence: 99%

Toward prediction of functional protein pockets using blind docking and pocket search algorithms

Hetényi

Spoel

2011

Protein Science

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“…The molecular surfaces of SLeX and B4GAL‐T1, along with the results of the docking simulations, were computed and visualized using VMD 41. AutoDock Tools (ADT) 4.2 was utilized to configure the simulation input files 42. SLeX and B4GAL‐T1 were converted into the PDBQT file format.…”

Section: Methodsmentioning

confidence: 99%

A Novel On‐Chip Method for Differential Extraction of Sperm in Forensic Cases

et al. 2018

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One out of every six American women has been the victim of a sexual assault in their lifetime. However, the DNA casework backlog continues to increase outpacing the nation's capacity since DNA evidence processing in sexual assault casework remains a bottleneck due to laborious and time‐consuming differential extraction of victim's and perpetrator's cells. Additionally, a significant amount (60–90%) of male DNA evidence may be lost with existing procedures. Here, a microfluidic method is developed that selectively captures sperm using a unique oligosaccharide sequence (Sialyl‐LewisX), a major carbohydrate ligand for sperm‐egg binding. This method is validated with forensic mock samples dating back to 2003, resulting in 70–92% sperm capture efficiency and a 60–92% reduction in epithelial fraction. Captured sperm are then lysed on‐chip and sperm DNA is isolated. This method reduces assay‐time from 8 h to 80 min, providing an inexpensive alternative to current differential extraction techniques, accelerating identification of suspects and advancing public safety.

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“…4), showed slightly reduced activity towards the target enzyme, compared to the reference C (IC 50 = 22 nM) when the OH-group on the benzoyl moiety was in the 4-position (compounds 27 and 28, tables 2 and 3). Moving the OHgroup to the 3-position, however, resulted in compounds 25 and 26 with higher activities (IC 50 = 104 nM and 275 nM, respectively). Thus, regarding the hydroxybenzoyl moiety, the SAR of these novel compounds with two linker functions appears to be similar to that discovered previously for compounds bearing the keto-linker group only.…”

Section: Modification Cmentioning

confidence: 98%

“…Also the bulky ether derivatives 23 and 24 strongly inhibited the target enzyme. All four compounds displayed similarly low IC 50 -values in the range of 90 nM to 157 nM (table 3), but no selectivity over the type 2 enzyme with the exception of compound 24 (SF = 5.5). Table 2 4.1.4.…”

Section: Modification Cmentioning

confidence: 99%

See 1 more Smart Citation

Inhibition of 17β-HSD1: SAR of bicyclic substituted hydroxyphenylmethanones and discovery of new potent inhibitors with thioether linker

Abdelsamie

Bey²,

Hanke³

et al. 2014

European Journal of Medicinal Chemistry

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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

Cited by 18,622 publications

References 18 publications

Toward prediction of functional protein pockets using blind docking and pocket search algorithms

Toward prediction of functional protein pockets using blind docking and pocket search algorithms

A Novel On‐Chip Method for Differential Extraction of Sperm in Forensic Cases

Inhibition of 17β-HSD1: SAR of bicyclic substituted hydroxyphenylmethanones and discovery of new potent inhibitors with thioether linker

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