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

Molecular Models02:00

Molecular Models

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.
Molecular Compounds: Formulas and Nomenclature03:10

Molecular Compounds: Formulas and Nomenclature

Molecular compounds or covalent compounds result when atoms share electrons to form covalent bonds. Since there is no electron transfer, molecular compounds do not contain ions; instead, they consist of discrete, neutral molecules.
Overview of Advanced Functional Groups02:22

Overview of Advanced Functional Groups


Functional groups are groups of atoms with specific chemical properties that occur within organic molecules and are sometimes denoted as “R”. Functional groups can “functionalize” a compound by enabling it to adopt different physical and chemical properties.
Types of Advanced Functional Groups
The table below summarizes some of the major functional groups in organic chemistry.
Molecular Comparison of Gases, Liquids, and Solids02:26

Molecular Comparison of Gases, Liquids, and Solids

Particles in a solid are tightly packed together (fixed shape) and often arranged in a regular pattern; in a liquid, they are close together with no regular arrangement (no fixed shape); in a gas, they are far apart with no regular arrangement (no fixed shape). Particles in a solid vibrate about fixed positions (cannot flow) and do not generally move in relation to one another; in a liquid, they move past each other (can flow) but remain in essentially constant contact; in a gas, they move...
Extraction: Partition and Distribution Coefficients01:14

Extraction: Partition and Distribution Coefficients

The distribution law or Nernst's distribution law is the law that governs the distribution of a solute between two immiscible solvents. This law, also known as the partition law, states that if a solute is added to the mixture of two immiscible solvents at a constant temperature, the solute is distributed between the two solvents in such a way that the ratio of solute concentrations in the solvents remains constant at equilibrium.
For extracting a solute from an aqueous phase into an organic...
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

You might also read

Related Articles

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

Sort by
Same author

The Role of Water in Protein-Ligand Binding: Decisive Factor, Annoying Feature, or Indispensable Control Element: In Any Case, a Major Challenge.

ChemMedChem·2026
Same author

Thermodynamic Data Remain a Hot Tip for Decoding Binding Affinity and Water Impact on Protein-Ligand Complex Formation to Assist Lead Optimization.

Journal of medicinal chemistry·2026
Same author

Natural Product-like Fragments Unlock Novel Chemotypes for a Kinase Target─Exploring Options beyond the Flatland.

Journal of chemical information and modeling·2025
Same author

Development of a Crystallographic Screening to Identify Sudan Virus VP40 Ligands.

ACS omega·2024
Same author

Fragment-Based Design, Synthesis, and Characterization of Aminoisoindole-Derived Furin Inhibitors.

ChemMedChem·2024
Same author

Crystallographic Fragment Screening on the <i>Shigella</i> Type III Secretion System Chaperone IpgC.

ACS omega·2023

Related Experiment Video

Updated: Jun 4, 2026

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids
08:04

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids

Published on: May 27, 2020

fconv: Format conversion, manipulation and feature computation of molecular data.

Gerd Neudert1, Gerhard Klebe

  • 1Department of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marburg, Germany.

Bioinformatics (Oxford, England)
|February 22, 2011
PubMed
Summary

fconv is a versatile molecular data processing program, offering robust tools for drug design workflows. It handles format conversion, cavity detection, and property calculations with enhanced atom type classification.

More Related Videos

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

Application of Unsupervised Multi-Omic Factor Analysis to Uncover Patterns of Variation and Molecular Processes Linked to Cardiovascular Disease
08:51

Application of Unsupervised Multi-Omic Factor Analysis to Uncover Patterns of Variation and Molecular Processes Linked to Cardiovascular Disease

Published on: September 20, 2024

Related Experiment Videos

Last Updated: Jun 4, 2026

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids
08:04

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids

Published on: May 27, 2020

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

Application of Unsupervised Multi-Omic Factor Analysis to Uncover Patterns of Variation and Molecular Processes Linked to Cardiovascular Disease
08:51

Application of Unsupervised Multi-Omic Factor Analysis to Uncover Patterns of Variation and Molecular Processes Linked to Cardiovascular Disease

Published on: September 20, 2024

Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Drug design

Background:

  • fconv is a mature, extensively tested program developed over three years.
  • It is integrated into drug design computational workflows.
  • The software is available under the GNU General Public License.

Purpose of the Study:

  • To present fconv as a comprehensive tool for molecular data manipulation.
  • To highlight its capabilities in drug design and computational chemistry.
  • To detail its functionalities including format conversion, property calculation, and atom type classification.

Main Methods:

  • Utilizes C++ for development.
  • Supports multiple molecular file formats (PDB(QT), MOL2, SDF, DLG, CIF).
  • Implements a unique, differentiated internal atom type classification system.

Main Results:

  • fconv performs tasks such as format conversion, error correction, ligand extraction, cavity detection, RMSD calculation, clustering, substructure searching, alignment, and crystal packing construction.
  • It calculates molecular properties including rotatable bonds, molecular weights, and vdW volumes.
  • Offers flexible atom type classification with predefined and user-definable mappings.

Conclusions:

  • fconv is a robust and comprehensive software tool for diverse computational chemistry and drug design tasks.
  • Its advanced atom type classification provides greater differentiation than standard methods.
  • The software is freely available with source code and executables for major operating systems.