<i>PRODRG</i>: a tool for high-throughput crystallography of protein–ligand complexes

Schüttelkopf, Alexander W.; Aalten, Daan M. F. van

doi:10.1107/s0907444904011679

Cited by 4,598 publications

(3,343 citation statements)

References 33 publications

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“…COOT [39], with restraint files generated by the PRODRG2 Server [40] where necessary. The coordinates and structure factors are available from the Protein Data Bank with PDB Accession codes,…”

Section: A C C E P T E D Accepted Manuscriptmentioning

confidence: 99%

Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions

Drinkwater

Vinh

Mistry

et al. 2016

European Journal of Medicinal Chemistry

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Section: A C C E P T E D Accepted Manuscriptmentioning

confidence: 99%

Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions

Drinkwater

Vinh

Mistry

et al. 2016

European Journal of Medicinal Chemistry

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“…We utilized Gromacs 4.6.2 (with the -missing flag when required) to get the non-bonded force parameters for all molecules except the drug sorafenib. For sorafenib we obtained the parameters through PRODRG server (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/) 44 . We conducted three docking simulations using Haptimol RD, and the respective geometry and force parameter files.…”

Section: Real-time Rigid-docking Simulationmentioning

confidence: 99%

A real-time proximity querying algorithm for haptic-based molecular docking

2014

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Intermolecular binding underlies various metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow us to study the binding process. Haptic-based docking provides an immersive virtual docking environment where the user can interact with and guide the molecules to their binding pose. Moreover, it allows human perception, intuition and knowledge to assist and accelerate the docking process, and reduces incorrect binding poses. Crucial for interactive docking is the real-time calculation of interaction forces. For smooth and accurate haptic exploration and manipulation, forcefeedback cues have to be updated at a rate of 1 kHz. Hence, force calculations must be performed within 1ms. To achieve this, modern haptic-based docking approaches often utilize pre-computed force grids and linear interpolation. However, such grids are time-consuming to pre-compute (especially for large molecules), memory hungry, can induce rough force transitions at cell boundaries and cannot be applied to flexible docking. Here we propose an efficient proximity querying method for computing intermolecular forces in real time. Our motivation is the eventual development of a haptic-based docking solution that can model molecular flexibility. Uniquely in a haptics application we use octrees to decompose the 3D search space in order to identify the set of interacting atoms within a cut-off distance. Force calculations are then performed on this set in real time. The implementation constructs the trees dynamically, and computes the interaction forces of large molecular structures (i.e. consisting of thousands of atoms) within haptic refresh rates. We have implemented this method in an immersive, haptic-based, rigid-body, molecular docking application called Haptimol RD. The user can use the haptic device to orientate the molecules in space, sense the interaction forces on the device, and guide the molecules to their binding pose. Haptimol RD is designed to run on consumer level hardware, i.e. there is no need for specialized/proprietary hardware.

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“…All moleculardynamics simulations were performed using the GRO-MACS suite of programs (version 4.0.5) [25] using the 43a1 force field. The initial coordinates and topology for HETATOM molecules were constructed with the PRODRG [26] web server. Complexes were placed into cubic box imposing a minimal distance between the solute and the box walls of 10.0 Å and solvated with SPC216 water model.…”

Section: Molecular Dynamicsmentioning

confidence: 99%

3D-QSAR studies of triazolopyrimidine derivatives of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors using a combination of molecular dynamics, docking, and genetic algorithm-based methods

Shah

Kumar

Tiwari³

et al. 2012

J Chem Biol

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A series of 35 triazolopyrimidine analogues reported as Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors were optimized using quantum mechanics methods, and their binding conformations were studied by docking and 3D quantitative structure-activity relationship studies. Genetic algorithm-based criteria was adopted for selection of training and test sets while maintaining structural diversity of training and test sets, which is also very crucial for model development and validation. Both the comparative molecular field analyses (q 2 LOO ¼ 0:841, r 2 ncv ¼ 0:99) and comparative molecular similarity indices analyses (q 2 LOO ¼ 0:757, r 2 ncv ¼ 0:943) show excellent correlation and high predictive power. Furthermore, molecular dynamics simulations were performed to explore the binding mode of the two of the most active compounds of the series, 10 and 14. Harmonization in the two simulation results validate the analysis and therefore applicability of docking parameters based on crystallographic conformation of compound 14 bound to receptor molecule. This work provides useful information about the inhibition mechanism of this class of molecules and will assist in the design of more potent inhibitors of PfDHODH.

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PRODRG: a tool for high-throughput crystallography of protein–ligand complexes

Cited by 4,598 publications

References 33 publications

Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions

Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions

A real-time proximity querying algorithm for haptic-based molecular docking

3D-QSAR studies of triazolopyrimidine derivatives of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors using a combination of molecular dynamics, docking, and genetic algorithm-based methods

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