DWARF – a data warehouse system for analyzing protein families

Fischer, Markus; Thai, Quan Ke; Grieb, Melanie; Pleiss, Jürgen

doi:10.1186/1471-2105-7-495

Cited by 59 publications

(26 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Sequence data is extracted from the NCBI protein database by BLAST (basic local alignment search tool) searches starting from as et of seed sequences. [40] Model-derived information for sequence data comprises hierarchical sorting of individual se- ChemBioChem 2016ChemBioChem , 17,2093ChemBioChem -2098 www.chembiochem.org quences into proteins and homologous families by the USEARCHc lustering algorithm, [41] sequence alignments generated by Clustal Omega, [42] the generation of family-specifics equencep rofiles by using hidden Markov models, [43] assignment of standard position numbers, [44] links to literature entries, [45] and the annotation of structurally or functionally relevant positions. Additionally,s tructure data can be used for homology modeling.…”

Section: Resultsmentioning

confidence: 99%

BioCatNet: A Database System for the Integration of Enzyme Sequences and Biocatalytic Experiments

et al. 2016

Self Cite

View full text Add to dashboard Cite

The development of novel enzymes for biocatalytic processes requires knowledge on substrate profile and selectivity; this can be derived from databases and from publications. Often, these sources lack time-course data for the substrate or product, and an unambiguous link between experiment and enzyme sequence. The lack of integrated, original data hampers the comprehensive analysis of enzyme kinetics and the evaluation of sequence-function relationships. In order to accelerate enzyme engineering, BioCatNet integrates protein sequence, protein structure, and experimental data for a given enzyme family. BioCatNet explicitly assigns the enzyme sequence to the experimental data, which consists of information on reaction conditions and time-course data. BioCatNet facilitates the consistent documentation of reaction conditions, the archiving of time-course data, and the efficient exchange of experimental data among collaborators. Data integration is demonstrated for three case studies by using the TEED (Thiamine diphosphate-dependent Enzymes Engineering Database).

show abstract

Section: Resultsmentioning

confidence: 99%

BioCatNet: A Database System for the Integration of Enzyme Sequences and Biocatalytic Experiments

et al. 2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…In comparison to the previous release [1] with 4322 protein and 167 structure entries this update represents a significant increase in data volume. By comparing CALA to representative structures from all superfamilies, a structure from the deacetylase superfamily was found to be most similar to the structure of CALA.…”

Section: Resultsmentioning

confidence: 99%

Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A

2010

Self Cite

View full text Add to dashboard Cite

BackgroundThe Lipase Engineering Database (LED) integrates information on sequence, structure and function of lipases, esterases and related proteins with the α/β hydrolase fold. A new superfamily for Candida antarctica lipase A (CALA) was introduced including the recently published crystal structure of CALA. Since CALA has a highly divergent sequence in comparison to other α/β hydrolases, the Lipase Engineering Database was used to classify CALA in the frame of the already established classification system. This involved the comparison of CALA to similar structures as well as sequence-based comparisons against the content of the LED.ResultsThe new release 3.0 (December 2009) of the Lipase Engineering Database contains 24783 sequence entries for 18585 proteins as well as 656 experimentally determined protein structures, including the structure of CALA. In comparison to the previous release [1] with 4322 protein and 167 structure entries this update represents a significant increase in data volume. By comparing CALA to representative structures from all superfamilies, a structure from the deacetylase superfamily was found to be most similar to the structure of CALA. While the α/β hydrolase fold is conserved in both proteins, the major difference is found in the cap region. Sequence alignments between both proteins show a sequence similarity of only 15%. A multisequence alignment of both protein families was used to create hidden Markov models for the cap region of CALA and showed that the cap region of CALA is unique among all other proteins of the α/β hydrolase fold. By specifically comparing the substrate binding pocket of CALA to other binding pockets of α/β hydrolases, the binding pocket of Candida rugosa lipase was identified as being highly similar. This similarity also applied to the lid of Candida rugosa lipase in comparison to the potential lid of CALA.ConclusionThe LED serves as a valuable tool for the systematic analysis of single proteins or protein families. The updated release 3.0 was used for the evaluation of α/β hydrolases. The HTML version of the database with new features is available at http://www.led.uni-stuttgart.de and provides sequences, structures and a set of analysis tools including phylogenetic trees and HMM profiles

show abstract

“…Esterases/lipases belong to the family of ␣/␤ hydrolases which share a highly conserved catalytic triad: a serine, histidine, and an aspartic acid or glutamic acid. A consensus signature sequence containing the active site serine is usually characterized by a conserved pentapeptide GXSXG motif [5,6]. In general, esterases have the ability to hydrolyze ester substrates with short-chain fatty acids (≤C10), whereas lipases hydrolyze long-chain fatty acids (≥C10) [7].…”

Section: Introductionmentioning

confidence: 99%

Characterization of a new thermophilic and acid tolerant esterase from Thermotoga maritima capable of hydrolytic resolution of racemic ketoprofen ethyl ester

Wei

Feng

Mao

et al. 2013

Journal of Molecular Catalysis B: Enzymatic

View full text Add to dashboard Cite

DWARF – a data warehouse system for analyzing protein families

Cited by 59 publications

References 32 publications

BioCatNet: A Database System for the Integration of Enzyme Sequences and Biocatalytic Experiments

BioCatNet: A Database System for the Integration of Enzyme Sequences and Biocatalytic Experiments

Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A

Characterization of a new thermophilic and acid tolerant esterase from Thermotoga maritima capable of hydrolytic resolution of racemic ketoprofen ethyl ester

Contact Info

Product

Resources

About