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Handling ligands with Coot.

ABSTRACT: Coot is a molecular-graphics application primarily aimed to assist in model building and validation of biological macromolecules. Recently, tools have been added to work with small molecules. The newly incorporated tools for the manipulation and validation of ligands include interaction with PRODRG, subgraph isomorphism-based tools, representation of ligand chemistry, ligand fitting and analysis, and are described here.

SUBMITTER: Debreczeni JE

PROVIDER: S-EPMC3322601 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature

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Handling ligands with Coot.

Debreczeni Judit É JÉ Emsley Paul P

Acta crystallographica. Section D, Biological crystallography 20120316 Pt 4

Coot is a molecular-graphics application primarily aimed to assist in model building and validation of biological macromolecules. Recently, tools have been added to work with small molecules. The newly incorporated tools for the manipulation and validation of ligands include interaction with PRODRG, subgraph isomorphism-based tools, representation of ligand chemistry, ligand fitting and analysis, and are described here. ...[more]

PMID: 22505262

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Project description:Background Although acoustic communication plays an essential role in the social interactions of Rallidae, our knowledge of how Rallidae encode diverse types of information using simple vocalizations is limited. We recorded and examined the vocalizations of a common coot (Fulica atra) population during the breeding season to test the hypotheses that 1) different call types can be emitted under different behavioral contexts, and 2) variation in the vocal structure of a single call type may be influenced both by behavioral motivations and individual signature. We measured a total of 61 recordings of 30 adults while noting the behavioral activities in which individuals were engaged. We compared several acoustic parameters of the same call type emitted under different behavioral activities to determine how frequency and temporal parameters changed depending on behavioral motivations and individual differences. Results We found that adult common coots had a small vocal repertoire, including 4 types of call, composed of a single syllable that was used during 9 types of behaviors. The 4 calls significantly differed in both frequency and temporal parameters and can be clearly distinguished by discriminant function analysis. Minimum frequency of fundamental frequency (F0min) and duration of syllable (T) contributed the most to acoustic divergence between calls. Call a was the most commonly used (in 8 of the 9 behaviors detected), and maximum frequency of fundamental frequency (F0max) and interval of syllables (TI) contributed the most to variation in call a. Duration of syllable (T) in a single call a can vary with different behavioral motivations after individual vocal signature being controlled. Conclusions These results demonstrate that several call types of a small repertoire, and a single call with function-related changes in the temporal parameter in common coots could potentially indicate various behavioral motivations and individual signature. This study advances our knowledge of how Rallidae use “simple” vocal systems to express diverse motivations and provides new models for future studies on the role of vocalization in avian communication and behavior. Supplementary Information The online version contains supplementary material available at 10.1186/s40850-021-00088-4.

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Handling ligands with Coot.

Publications

Handling ligands with Coot.

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