Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

12.9K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.9K
Protein Organization01:24

Protein Organization

6.5K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
6.5K
Molecular Models02:00

Molecular Models

38.5K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
38.5K
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

43.8K
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...
43.8K
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.5K
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...
12.5K
Protein and Protein Structures02:15

Protein and Protein Structures

10.6K
10.6K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

NG2-ITGA4 axis regulates Rho GTPases and leukemic aggressiveness in KMT2A-r B-ALL and is targetable with natalizumab.

Blood·2026
Same author

Experimentally validated deep learning control of protein aggregation.

Communications chemistry·2026
Same author

Oxidative stress-driven transcriptomic remodeling in human astrocytes reveals network signatures associated with neurodegenerative and cardiovascular processes.

Computational and structural biotechnology journal·2026
Same author

Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.

Communications biology·2025
Same author

Predicting cellular adaptation proteins dependent on eIF2α regulation under stress conditions: Physiological and pathophysiological implications in neuronal function.

Computational and structural biotechnology journal·2025
Same author

Computational Design and Evaluation of Peptides to Target SARS-CoV-2 Spike-ACE2 Interaction.

Molecules (Basel, Switzerland)·2025

Related Experiment Video

Updated: Jul 14, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

1.9K

SBILib: a handle for protein modeling and engineering.

Patrick Gohl1, Jaume Bonet1, Oriol Fornes2

  • 1Department of Medicine and Life Sciences, SBI-GRIB, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.

Bioinformatics (Oxford, England)
|October 5, 2023
PubMed
Summary

SBILib is a Python library for analyzing macromolecular structures and interactions. It offers tools for parsing 3D files, analyzing protein structures, and comparing complexes, enhancing biological data analysis.

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.1K
Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

12.7K

Related Experiment Videos

Last Updated: Jul 14, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

1.9K
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.1K
Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

12.7K

Area of Science:

  • Structural Bioinformatics
  • Computational Biology
  • Biochemistry

Background:

  • Macromolecular structure and interaction analysis is crucial for understanding biological processes.
  • Existing tools may lack integrated functionalities for diverse analytical tasks.
  • A unified platform can streamline complex structural bioinformatics workflows.

Purpose of the Study:

  • To introduce SBILib, a Python library designed for integrated analysis of macromolecular structures and interactions.
  • To provide a comprehensive suite of tools for parsing, analyzing, and comparing protein and nucleic acid complexes.
  • To facilitate the study of protein super-secondary structures and loop geometry.

Main Methods:

  • Development of a Python library (SBILib) with modules for macromolecular interactions, loops, super-secondary structures, and biological sequences.
  • Implementation of 3D file parsing and workup methods.
  • Integration of wrappers for external tools to enable comparative analysis.
  • Capability to handle complexes of proteins, DNA, and RNA.

Main Results:

  • SBILib offers an integrated platform for analyzing macromolecular structures and interactions.
  • The library uniquely parses and calculates protein super-secondary structure and loop geometry.
  • It supports comparative analysis of protein structures and complexes, including those with nucleic acids.
  • Example scenarios for SBILib application are provided within the library.

Conclusions:

  • SBILib provides a versatile and integrated solution for structural bioinformatics analyses.
  • The library enhances the comparative analysis of macromolecular structures and complexes.
  • Its unique capabilities in super-secondary structure and loop geometry analysis offer significant advantages.