A Survey of Remote Homology Detection and Fold Recognition Methods

Rangwala, Huzefa

doi:10.1002/9780470882207.ch8

Cited by 2 publications

(3 citation statements)

References 78 publications

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“…Knowledge based methods for protein and peptide modeling use comparative statistical analysis to predict the structure of the amino acid sequence of the target protein from (i) the sequence of homologous proteins of known structure; or (ii) a database of protein structures (Rangwala 2010). The accuracy of this approach relies on the current knowledge of protein structures and evolutionary relationships.…”

Section: Knowledge Based Methodsmentioning

confidence: 99%

Polypeptide and Protein Modeling for Drug Design

O’Mara

Deplazes²

2015

Encyclopedia of Computational Neuroscience

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Computational modeling, structure-aided drug design, computational structural biology DefinitionModeling of polypeptides and proteins, often referred to as biomolecular or molecular modeling, encompasses the use of theoretical models and computational methods to model the structure and dynamics of molecules of biological interest such as peptides, proteins and small organic molecules (ligands).The aims of protein and peptide modeling for drug design include: (i) modeling the threedimensional structure of proteins of current or potential drug targets; (ii) identifying and characterizing the structural dynamics associated with the function of a particular protein or peptide; and (iii) predicting the structure and molecular interactions of protein-ligand complexes. This knowledge underpins structure-based and rational drug design. It can aid in the design and optimization of drug molecules by shedding light on their mode of action, specificity and selectivity.

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Section: Knowledge Based Methodsmentioning

confidence: 99%

Polypeptide and Protein Modeling for Drug Design

O’Mara

Deplazes²

2015

Encyclopedia of Computational Neuroscience

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“…However, bijective functions allow only 1-1 matching and, in some cases, this may be not enough. For example, in the study of remote homologous proteins [9] (i.e., proteins having a pairwise sequence identity lower than 25%), it may be necessary to study protein similarities based on different kinds of amino acid property, such as chemical behavior or protein profiles, thus resulting in the necessity to allow many-to-many matches among amino acids. As a further example, bijective matching functions between words may miss common situations while comparing bilingual text corpora, where different words share the same meaning; for instance, English words Hello and Goodbye can be both interchangeably matched with Italian words Ciao, Salve, and Addio.…”

Section: Introductionmentioning

confidence: 99%

“…1 ≤ | 1 | and 0 < π 2 ≤ | 2 |; the Multi-Parameterized Edit Distance between s 1 and s 2 (L π 1 ,π 2 ,χ (s 1 , s 2 ), for short)is the minimum distance that can be obtained with any π 1 , π 2 , χ -constrained matching schema and any alignment s 1 ,s 2 . Formally:A L = 1 , 2 , π 1 , π 2 , χ , M, L M (•, •)(8)andF L (s 1 , s 2 ) = L π 1 ,π 2 ,χ (s 1 , s 2 ) = min M π 1 ,π 2 ,χ ∈M {L M (s 1 , s 2 )}(9) …”

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confidence: 99%

A General Approach to Uniformly Handle Different String Metrics Based on Heterogeneous Alphabets

et al. 2020

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In the last few years, we have assisted in a great increase of the usage of strings in the most disparate areas. In the meantime, the development of the Internet has brought the necessity of managing strings from very different contexts and possibly using different alphabets. This issue is not addressed by the numerous string comparison metrics previously proposed in the literature. In this paper, we aim at providing a contribution in this context. In fact, first we propose an approach to measure the similarity of strings based on different alphabets. Then we show that our approach can be specifically adapted to several classic string comparison metrics and that each specialization can lead to addressing completely different issues.

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A Survey of Remote Homology Detection and Fold Recognition Methods

Cited by 2 publications

References 78 publications

Polypeptide and Protein Modeling for Drug Design

Polypeptide and Protein Modeling for Drug Design

A General Approach to Uniformly Handle Different String Metrics Based on Heterogeneous Alphabets

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