PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules

Aalten, D.M.F. van; Bywater, Robert P.; Findlay, John B. C.; Hendlich, Manfred; Hooft, Rob; Vriend, Gerrit

doi:10.1007/bf00355047

Cited by 656 publications

(397 citation statements)

References 15 publications

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“…34 Topology files were generated from initial structures, in Cartesian coordinates, resorting to the PRODRG server. 35 The polymer and gemini surfactants were added to a box and solvated with single point charge (SPC) model water, 36 with their structure constrained by the SETTLE algorithm. 37 Five different simulations were conducted as summarized in Table 3.…”

Section: Methodsmentioning

confidence: 99%

Interplay of Electrostatic and Hydrophobic Effects with Binding of Cationic Gemini Surfactants and a Conjugated Polyanion: Experimental and Molecular Modeling Studies

et al. 2007

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Understanding factors responsible for the fluorescence behavior of conjugated polyelectrolytes and modulation of their behavior are important for their application as functional materials. The interaction between the anionic poly{1,4-phenylene-[9,9-bis(4-phenoxy-butylsulfonate)]fluorene-2,7-diyl}copolymer (PBS-PFP) and cationic gemini surfactants R,ω-(C m H 2m+1 N + (CH 3 ) 2 ) 2 (CH 2 ) s (Br -) 2 (m-s-m; m ) 12, s ) 2, 3, 5, 6, 10, and 12) has been studied experimentally in aqueous solution. These surfactants are chosen to see whether molecular recognition and self-assembly occurs between the oppositely charged conjugated polyelectrolyte and gemini surfactant when the spacer length on the surfactant is similar to the intercharge separation on the polymer. Without surfactants, PBS-PFP exists as aggregates. These are broken up upon addition of gemini surfactants. However, as anticipated, the behavior strongly depends upon spacer length (s). Fluorescence measurements show three surfactant concentration regimes: At low concentrations (<2 × 10 -6 M) quenching occurs and is most marked with the small spacer 12-2-12; at intermediate concentrations (∼2 × 10 -6 -10 -3 M), fluorescence intensity is constant, with a 12-carbon spacer 12-12-12 showing the strongest fluorescence; above the critical micelle concentration (CMC; ∼10 -3 M) increases in emission intensity are seen in all cases and are largest with the intermediate spacers 12-5-12 and 12-6-12, where the spacer length most closely matches the distance between monomer units on the polymer. With longer spacer length surfactants, surface tension measurements for concentrations below the CMC reveal the presence of polymer-surfactant aggregates at the air-water interface, possibly reflecting increased hydrophobicity. Above the CMC, small-angle neutron scattering experiments for the 12-6-12 system show the presence of spherical aggregates, both for the pure surfactant and for polyelectrolyte/gemini mixtures. Molecular dynamics simulations help rationalize these observations and show that there is a very fine balance between electrostatic and hydrophobic interactions. With the shortest spacer 12-2-12, Coulombic interactions are dominant, while for the longest spacer 12-12-12 the driving force involves hydrophobic interactions. Qualitatively, with the intermediate 12-5-12 and 12-6-12 systems, the optimum balance is observed between Coulombic and hydrophobic interactions, explaining their strong fluorescence enhancement.

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Section: Methodsmentioning

confidence: 99%

Interplay of Electrostatic and Hydrophobic Effects with Binding of Cationic Gemini Surfactants and a Conjugated Polyanion: Experimental and Molecular Modeling Studies

et al. 2007

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“…Refinement was performed with CNS (34) interspersed with model building in O (35). Topologies for the allosamidins were obtained from the PRODRG server (36). The inhibitors were not included until defined by unbiased ԽF o Խ Ϫ ԽF c Խ, calc maps (Fig.…”

Section: Methodsmentioning

confidence: 99%

“…A cut-off of 0.3 was applied here to exclude weak hydrogen bonds. Inhibitor hydrogen bonding potential was calculated with PRODRG (36). Donor acceptor distances in Å are also listed (D-A).…”

Section: Table IV Hcht-inhibitor Hydrogen Bondsmentioning

confidence: 99%

Crystal Structures of Allosamidin Derivatives in Complex with Human Macrophage Chitinase

Rao

Houston

Boot

et al. 2003

Journal of Biological Chemistry

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The pseudotrisaccharide allosamidin is a potent family 18 chitinase inhibitor with demonstrated biological activity against insects, fungi, and the Plasmodium falciparum life cycle. The synthesis and biological properties of several derivatives have been reported. The structural interactions of allosamidin with several family 18 chitinases have been determined by x-ray crystallography previously. Here, a high resolution structure of chitotriosidase, the human macrophage chitinase, in complex with allosamidin is presented. In addition, complexes of the allosamidin derivatives demethylallosamidin, methylallosamidin, and glucoallosamidin B are described, together with their inhibitory properties. Similar to other chitinases, inhibition of the human chitinase by allosamidin derivatives lacking a methyl group is 10-fold stronger, and smaller effects are observed for the methyl and C3 epimer derivatives. The structures explain the effects on inhibition in terms of altered hydrogen bonding and hydrophobic interactions, together with displaced water molecules. The data reported here represent a first step toward structurebased design of specific allosamidin derivatives.

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“…In this case, the user is responsible for preparing the simulation system. Web portals such as PRODRG, 39 Automated Topology Builder (ATB), 40 SwissParam, 41 and AnteChamber 42 can be used to generate topology and parameter files for nonstandard molecules.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

Dijk

Wassenaar

Bonvin

2012

J. Chem. Theory Comput.

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Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However, performing a successful simulation requires sufficient computational resources, familiarity with the simulation software, and experience in the setup of a system and the analysis of the resulting trajectories. These considerations become especially critical in large-scale parametric MD simulations. Offering such tools to a wide user community requires a robust and versatile, but user-friendly, facility for molecular dynamics simulations with access to vast computational resources. Here, we present the GROMACS grid-enabled Web portal for the setup and execution of molecular dynamics simulation on the WeNMR grid infrastructure, a distributed network of computational resources within the European Grid Initiative. The Web portal aims at ease-of-use through automated setup of the simulation system using bestpractice protocols, yet allowing for tuning of key parameters. Alternatively, the simulation can be started from preconfigured GROMACS simulation systems. Performing multiple lengthy calculations using multiple processors on the WeNMR grid infrastructure ensures scalability. The combination of analysis routines for quality assurance and automatic recovery in case of failures provides a reliable platform for MD simulations. The GROMACS Web portal is embedded within the services of the WeNMR Virtual Research Community (VRC) accessible from http://www.wenmr.eu/wenmr/nmr-services. It is freely accessible upon registration with a valid X509 personal certificate with the enmr.eu Virtual Organization (VO).

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PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules

Cited by 656 publications

References 15 publications

Interplay of Electrostatic and Hydrophobic Effects with Binding of Cationic Gemini Surfactants and a Conjugated Polyanion: Experimental and Molecular Modeling Studies

Interplay of Electrostatic and Hydrophobic Effects with Binding of Cationic Gemini Surfactants and a Conjugated Polyanion: Experimental and Molecular Modeling Studies

Crystal Structures of Allosamidin Derivatives in Complex with Human Macrophage Chitinase

A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

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