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Related Concept Videos

Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Fischer Projections02:18

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
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.
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
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Molecular Shapes01:18

Molecular Shapes

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...

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Modeling an Enzyme Active Site using Molecular Visualization Freeware
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Published on: December 25, 2021

HELM: a hierarchical notation language for complex biomolecule structure representation.

Tianhong Zhang1, Hongli Li, Hualin Xi

  • 1Pfizer Inc., 35 Cambridge Park Drive, Cambridge, Massachusetts 02140, USA. Tianhong.Zhang@pfizer.com

Journal of Chemical Information and Modeling
|September 6, 2012
PubMed
Summary
This summary is machine-generated.

Representing complex therapeutic biomolecules requires a new approach. The Hierarchical Editing Language for Macromolecules (HELM) provides a standardized method for describing these intricate chemical structures, improving data management for drug development.

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Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Drug Discovery

Background:

  • Biological macromolecules are increasingly used as therapeutic agents.
  • Non-natural chemical modifications are often required to enhance pharmaceutical properties.
  • Complex structures involving linked biomolecules and modified moieties pose representation challenges.

Purpose of the Study:

  • To introduce a novel language for representing complex biomolecules.
  • To address the limitations of atomic-level and sequence-only representations.
  • To demonstrate the utility of the Hierarchical Editing Language for Macromolecules (HELM) in drug development.

Main Methods:

  • Development of the Hierarchical Editing Language for Macromolecules (HELM).
  • Application of HELM to represent diverse complex biomolecular structures.
  • Demonstration of HELM's utility for electronic registration, storage, analysis, and visualization.

Main Results:

  • HELM enables accurate in silico representation of complex biomolecules.
  • The language effectively handles structures with non-natural chemical modifications.
  • HELM is demonstrated to be useful for representing antisense oligonucleotides, short interference RNAs, peptides, proteins, and antibody drug conjugates.

Conclusions:

  • HELM provides a robust and standardized solution for representing complex therapeutic macromolecules.
  • This standardized representation facilitates data management and analysis in pharmaceutical research.
  • HELM is essential for the accurate electronic registration and handling of advanced biologic drugs.