PRODRG: a tool for high-throughput crystallography of protein–ligand complexes
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Cites methods from "PRODRG: a tool for high-throughput ..."
...Topology and parameter files for the inhibitors were generated by using PRODRG (39)....
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...Schuttelkopf AW, van Aalten DM (2004) PRODRG: A tool for high-throughput crystallography of protein-ligand complexes....
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References
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Additional excerpts
...…re®nement/model-building programs [X-PLOR (BruÈ nger, 1988), CNS (BruÈ nger et al., 1998), REFMAC5 (Murshudov et al., 1997), SHELX (Sheldrick & Schneider, 1997) and O (Jones et al., 1991)] as well as docking programs [AutoDock 2.4/3.0 (Morris et al., 1996, 1998), Hex (Ritchie & Kemp, 2000)]....
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...…re®nement/model-building programs [X-PLOR (BruÈ nger, 1988), CNS (BruÈ nger et al., 1998), REFMAC5 (Murshudov et al., 1997), SHELX (Sheldrick & Schneider, 1997) and O (Jones et al., 1991)] as well as docking programs [AutoDock 2.4/3.0 (Morris et al., 1996, 1998), Hex (Ritchie & Kemp, 2000)]....
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"PRODRG: a tool for high-throughput ..." refers methods in this paper
...0.04 information was generated, followed by energy minimization with the generated topology in the GROMACS package....
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...A particular focus is the implementation of a new coordinate-generating mechanism which will remove the dependency on GROMACS from PRODRG, speed up coordinate production and, most importantly, open a path towards the use of different/novel force ®elds....
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...The H-atom assignment is followed by the generation of a topology for use with GROMACS (Berendsen et al., 1995; Lindahl et al., 2001)....
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...The dependence of PRODRG on GROMACS (the GROMOS87 force ®eld) leads to a number of limitations in the scope of compounds that PRODRG can handle....
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...Energy minimization is performed by steepest descent for at most 50 000 steps, with the ffgmx GROMACS force ®eld, extended by 11 additional atom types to accommodate halogens, sp-hybridized atoms and other chemical features....
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1,006 citations
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...…re®nement/model-building programs [X-PLOR (BruÈ nger, 1988), CNS (BruÈ nger et al., 1998), REFMAC5 (Murshudov et al., 1997), SHELX (Sheldrick & Schneider, 1997) and O (Jones et al., 1991)] as well as docking programs [AutoDock 2.4/3.0 (Morris et al., 1996, 1998), Hex (Ritchie & Kemp, 2000)]....
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716 citations
"PRODRG: a tool for high-throughput ..." refers background in this paper
...The protein±drug interaction then needs to be examined in terms of detailed hydrogen-bonding geometry or other scoring functions (reviewed in Brooijmans & Kuntz, 2003)....
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