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Related Concept Videos

Protein and Protein Structure02:15

Protein and Protein Structure

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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ATP Synthase: Structure01:18

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ATP synthase or ATPase is among the most conserved proteins found in bacteria, mammals, and plants. This enzyme can catalyze a forward reaction in response to the electrochemical gradient, producing ATP from ADP and inorganic phosphate. ATP synthase can also work in a reverse direction by hydrolyzing ATP and generating an electrochemical gradient. Different forms of ATP synthases have evolved special features to meet the specific demands of the cell. Based on their specific feature, ATP...
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Drug Dissolution: Requirements and Profile Comparison01:14

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The acceptance criteria for dissolution profile data are anchored in Q values, representing the percentage of drug dissolved within a specified period. This assessment unfolds in three stages:First Stage: The test passes if all six drug dosage units are equal to or greater than Q plus 5%; otherwise, the sample proceeds to the second stage.Second Stage: The average of twelve units must be equal to or greater than Q, with no unit falling below Q - 15% to pass; if not, it progresses to the final...
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Conserved Binding Sites01:49

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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The bonds of adenosine triphosphate (ATP) can be broken through the addition of water, releasing one or two phosphate groups in an exergonic process called hydrolysis. This reaction liberates the energy in the bonds for use in the cell—for instance, to synthesize proteins from amino acids.
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ATP Yield01:31

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A Protocol for Computer-Based Protein Structure and Function Prediction
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ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based

Jun Hu1,2, Yang Li1,2, Yang Zhang2

  • 1School of Computer Science and Engineering, Nanjing University of Science and Technology , Xiaolingwei 200, Nanjing, 210094, P. R. China.

Journal of Chemical Information and Modeling
|January 24, 2018
PubMed
Summary

Identifying adenosine triphosphate (ATP) binding sites on proteins is crucial for understanding biological processes and drug development. The new ATPbind predictor accurately identifies these sites by integrating multiple data sources and machine learning models.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein-adenosine triphosphate (ATP) interactions are fundamental to numerous biological functions.
  • Accurate identification of ATP binding sites is vital for protein function annotation and drug discovery.
  • Existing methods lack optimal performance in predicting ATP binding sites across diverse proteins.

Purpose of the Study:

  • To develop a novel, composite predictor named ATPbind for identifying ATP binding sites.
  • To improve the accuracy and coverage of ATP binding site prediction compared to existing methods.

Main Methods:

  • Integrated outputs from template-based predictors (S-SITE, TM-SITE) with sequence-driven features (position-specific scoring matrix, predicted secondary structure, predicted solvent accessibility).
  • Employed multiple support vector machines (SVMs) with random undersampling to address data imbalance.
  • Constructed a gold-standard benchmark dataset of 429 ATP binding proteins from the Protein Data Bank (PDB).

Main Results:

  • ATPbind achieved an average accuracy of 72% and covered 62% of all ATP binding sites.
  • Demonstrated a significantly higher Matthews correlation coefficient compared to other state-of-the-art predictors.
  • Evaluated performance using a newly constructed benchmark dataset.

Conclusions:

  • ATPbind offers a superior method for identifying ATP binding sites in proteins.
  • The predictor's performance is validated against existing methods and a robust benchmark dataset.
  • This advancement aids in protein function annotation and accelerates drug discovery efforts.