Rapid protein structure classification using one-dimensional structure profiles on the BioSCAN parallel computer

Hoffman, Doug; Laiter, Sergei; Singh, Raj Kumar; Vaisman, Iosif I.; Tropsha, Alexander

doi:10.1093/bioinformatics/11.6.675

Cited by 2 publications

(3 citation statements)

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“…Cellular functions are regulated at different levels through transcription, signal transduction and protein modification [2][3][4][5][6][7]. To understand the complexity of a biological system, a reductionist approach is taken to study its organization, components and the interrelationships among these components: information about genes and their structures are obtained by genome sequencing and analysis [8][9][10]; gene regulation is studied by microarray analysis [11]; and protein functions are studied by proteomics [12], protein-protein interactions [13][14][15][16] and structure analysis [15,[17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32]. The huge amount of data generated by these new technologies needs to be analyzed and integrated to depict comprehensively how biological systems work.…”

Section: Introductionmentioning

confidence: 99%

Engineering Approaches Toward Biological Information Integration at the Systems Level

Zheng¹

2006

CBIO

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Our understanding of biological systems has improved dramatically due to decades of exploration. This process has been accelerated even further during the past ten years, mainly due to the genome projects, new technologies such as microarray, and developments in proteomics. These advances have generated huge amounts of data describing biological systems from different aspects. Still, integrating this knowledge to reconstruct a biological system in silico has been a significant challenge for biologists, computer scientists, engineers, mathematicians and statisticians. Engineering approaches toward integrating biological information can provide many advantages and capture both the static and dynamic information of a biological system. Methodologies, documentation and project management from the engineering field can be applied. This paper discusses the process, knowledge representation and project management involved in engineering approaches used for biological information integration, mainly using software engineering as an example. Developing efficient courses to educate students to meet the demands of this interdisciplinary approach will also be discussed.

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Section: Introductionmentioning

confidence: 99%

Engineering Approaches Toward Biological Information Integration at the Systems Level

Zheng¹

2006

CBIO

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“…Recently, for example, distributions of C -C distances were used to get onedimensional representations of protein structures [50,51] and Gauss integrals were employed to describe polypeptide chains and their proximity [52]. Also several other methods have been designed to describe three-dimensional objects with one-dimensional representations [53][54][55][56][57][58][59][60][61].…”

Section: Local Feature Frequency Profilementioning

confidence: 99%

“…Using these quantities, Ferrin and co-workers defined the following three measures of alignment similarity (54) where the sum is performed over all the residues belonging to the set R either (S2,A1,A2). …”

Section: Comparison Between Alternative Alignmentsmentioning

confidence: 99%

Recent Progress in Measuring Structural Similarity Between Proteins

Carugo

2007

CPPS

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Surprisingly, after at least two decades of researches focused on the analysis of the similarity between protein three-dimensional structures, several new comparison methods were proposed during the last few years. These are briefly summarized and commented below. Some of the newly developed techniques are fast and were designed to handle large amounts of data and vast structural databases. Other methods are much slower and were developed to gain biological information by comparing distantly related protein structures. Additional studies were devoted to the problem of the multiple structural alignments and to strategies of comparison between alternative structural alignments.

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Rapid protein structure classification using one-dimensional structure profiles on the BioSCAN parallel computer

Cited by 2 publications

References 0 publications

Engineering Approaches Toward Biological Information Integration at the Systems Level

Engineering Approaches Toward Biological Information Integration at the Systems Level

Recent Progress in Measuring Structural Similarity Between Proteins

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