Related Experiment Video
Updated: May 28, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Persistence and availability of Web services in computational biology
Sebastian J Schultheiss1, Marc-Christian Münch, Gergana D Andreeva
1Machine Learning in Biology Research Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany. sebastian.schultheiss@tue.mpg.de
Plos One
|October 4, 2011
Summary
Most bioinformatics web services remain available, but many lack reliable functionality and maintenance plans. Persistent addresses and code repositories can improve service longevity and impact.
Area of Science:
- Bioinformatics
- Computational Biology
- Scientific Web Services
Background:
- Assessing the long-term availability and functionality of bioinformatics web services is crucial for reproducible research.
- Many bioinformatics tools are developed by researchers without permanent positions, raising concerns about their sustained maintenance.
Purpose of the Study:
- To evaluate the long-term availability and functionality of bioinformatics web services.
- To identify factors predicting service survival and citation rates.
- To propose strategies for improving web service reliability and longevity.
Main Methods:
- Analysis of 927 bioinformatics web services published between 2003-2009.
- Functionality testing of available services.
- Survey of corresponding authors regarding service development and maintenance.
Main Results:
- 72% of web sites remain available, with 9% completely unavailable.
- Only 45% of services had confirmed functionality; 13% were non-functional.
- 78% of services were developed by non-permanent staff, and 24% lacked maintenance plans.
- A quality scoring system correlated with citation rates (1.8x more for high-scoring services).
Conclusions:
- Bioinformatics web services face challenges in long-term availability and functionality.
- Persistent web addresses and public code repositories are key to service sustainability.
- A quality scoring system can guide developers and reviewers to improve service reliability and impact.
Related Concept Videos
02:04Protein-protein Interfaces
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:21Globular and Fibrous Proteins
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
01:49Conserved Binding Sites
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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
01:49Conserved Binding Sites
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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...