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DNA as a Genetic Template

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...

DNA as a Genetic Template

DNA as a Genetic Template

Lewis Acids and Bases

Lewis Acids and Bases

In 1923, G. N. Lewis proposed a generalized definition of acid-base behavior in which acids and bases are identified by their ability to accept or to donate a pair of electrons and form a coordinate covalent bond.
A coordinate covalent bond (or dative bond) occurs when one of the atoms in the bond provides both bonding electrons. For example, a coordinate covalent bond occurs when a water molecule combines with a hydrogen ion to form a hydronium ion. A coordinate covalent bond also results when...

Weak Base Solutions

Weak Base Solutions

Some compounds produce hydroxide ions when dissolved by chemically reacting with water molecules. In all cases, these compounds react only partially and so are classified as weak bases. These types of compounds are also abundant in nature and important commodities in various technologies. For example, global production of the weak base ammonia is typically well over 100 metric tons annually, being widely used as an agricultural fertilizer, a raw material for chemical synthesis of other...

Base Excision Repair

Base Excision Repair

One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...

Ions as Acids and Bases

Ions as Acids and Bases

Salts with Acidic Ions
Salts are ionic compounds composed of cations and anions, either of which may be capable of undergoing an acid or base ionization reaction with water. Aqueous salt solutions, therefore, may be acidic, basic, or neutral, depending on the relative acid-base strengths of the salt’s constituent ions. For example, dissolving the ammonium chloride in water results in its dissociation, as described by the equation:

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Updated: Feb 9, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Protein alignment based on higher order conditional random fields for template-based modeling.

Juan A Morales-Cordovilla¹, Victoria Sanchez¹, Martin Ratajczak²

¹Dept. of Teoría de la Señal Telemática y Comunicaciones, Universidad de Granada, Granada, Spain.

|June 2, 2018

Summary

This summary is machine-generated.

This study introduces higher order Conditional Random Fields for improved query-template protein alignment, enhancing 3D protein structure prediction, especially for difficult, distantly-related protein pairs.

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A Protocol for Computer-Based Protein Structure and Function Prediction

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Area of Science:

Computational Biology
Bioinformatics
Structural Biology

Background:

Query-template alignment is crucial for template-based protein 3D structure prediction.
First-order Conditional Random Fields (CRFs) have shown success in protein alignment.
Higher-order CRFs have benefited other structured prediction tasks by capturing label correlations.

Purpose of the Study:

To propose and evaluate higher-order Conditional Random Fields for query-template protein alignment.
To improve the accuracy of protein structure prediction methods.

Main Methods:

Implementation and application of higher-order Conditional Random Fields for protein alignment.
Experimental validation on diverse public protein datasets.

Main Results:

Higher-order CRFs demonstrate improved performance in query-template protein alignment.
Significant gains observed particularly for distantly-related protein pairs, which are challenging to align.

Conclusions:

Higher-order CRFs represent a promising advancement for query-template protein alignment.
This approach enhances the reliability of template-based protein structure modeling, especially in challenging cases.