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List of works by Daniel J. Rigden

6-Phosphofructo-2-kinase and fructose-2,6-bisphosphatase in Trypanosomatidae. Molecular characterization, database searches, modelling studies and evolutionary analysis

scientific article

<i>findMySequence</i>: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM

scientific article published on 01 December 2021

A distant evolutionary relationship between GPI-specific phospholipase D and bacterial phosphatidylcholine-preferring phospholipase C.

scientific article published in July 2004

A diverse family of serine proteinase genes expressed in cotton boll weevil (Anthonomus grandis): implications for the design of pest-resistant transgenic cotton plants

scientific article published in September 2004

A new family of bacterial DNA repair proteins annotated by the integration of non-homology, distant homology and structural bioinformatic methods

scientific article

A new type of antimicrobial protein with multiple histidines from the hard tick, Amblyomma hebraeum

scientific article published on 9 July 2004

A novel heterodimeric antimicrobial peptide from the tree-frog Phyllomedusa distincta

scientific article published on 01 April 2001

A structural model for the rolA protein and its interaction with DNA.

scientific article

AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models

scientific article published on 9 November 2012

ATG24 Represses Autophagy and Differentiation and Is Essential for Homeostasy of the Flagellar Pocket in Trypanosoma brucei

scientific article published on 19 June 2015

Ab Initio Modeling Led Annotation Suggests Nucleic Acid Binding Function for Many DUFs ⬇️

scientific article published on February 24, 2011

Ab initio protein modelling reveals novel human MIT domains

scientific article

Active-site characterization of Candida boidinii formate dehydrogenase

scientific article

Activity of wheat alpha-amylase inhibitors towards bruchid alpha-amylases and structural explanation of observed specificities.

scientific article

Acyl carrier protein phosphodiesterase (AcpH) of Escherichia coli is a non-canonical member of the HD phosphatase/phosphodiesterase family.

scientific article published in January 2007

Alternate Structural Conformations of Streptococcus pneumoniae Hyaluronan Lyase: Insights into Enzyme Flexibility and Underlying Molecular Mechanism of Action

scientific article published on 13 March 2006

Amidase domains from bacterial and phage autolysins define a family of gamma-D,L-glutamate-specific amidohydrolases

scientific article published in May 2003

An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands

scientific article published on 01 April 2003

An unsuspected ecdysteroid/steroid phosphatase activity in the key T-cell regulator, Sts-1: surprising relationship to insect ecdysteroid phosphate phosphatase

scientific article

Analysis of Structure and Function of Putative Surface-Exposed Proteins Encoded in the Streptococcus pneumoniae Genome: A Bioinformatics-Based Approach to Vaccine and Drug Design ⬇️

scientific article published on January 1, 2003

Analysis of glycoside hydrolase family 98: catalytic machinery, mechanism and a novel putative carbohydrate binding module

article

Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement.

scientific article

Applications of contact predictions to structural biology

scientific article

Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

scientific article published on 22 November 2017

Archaea recruited D-Tyr-tRNATyr deacylase for editing in Thr-tRNA synthetase

scientific article published on 3 November 2004

Assessing the utility of <scp>CASP14</scp> models for molecular replacement

scientific article published in 2021

Autophagy and related processes in trypanosomatids: insights from genomic and bioinformatic analyses

scientific article published on 2 April 2006

Autophagy in parasitic protists: unique features and drug targets

scientific article published on 21 February 2011

Autophagy in protists.

scientific article published on February 2011

Autophagy in protists: Examples of secondary loss, lineage-specific innovations, and the conundrum of remodeling a single mitochondrion

scientific article published on 24 August 2009

Autophosphorylation is a mechanism of inhibition in twitchin kinase

scientific article published on 3 February 2018

Beta-helical catalytic domains in glycoside hydrolase families 49, 55 and 87: domain architecture, modelling and assignment of catalytic residues.

scientific article published in October 2002

Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics

scientific article published on 13 June 2020

Biophysical Analysis of the N-Terminal Domain from the Human Protein Phosphatase 1 Nuclear Targeting Subunit PNUTS Suggests an Extended Transcription Factor TFIIS-Like Fold ⬇️

scientific article

CARP interacts with titin at a unique helical N2A sequence and at the domain Ig81 to form a structured complex

scientific article

CUCU modification of mRNA promotes decapping and transcript degradation in Aspergillus nidulans.

scientific article published on 9 November 2009

Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae

scientific article published on 13 February 2018

Cathepsin L digestion of nanobioconjugates upon endocytosis

scientific article published in September 2009

Characterisation of a desmosterol reductase involved in phytosterol dealkylation in the silkworm, Bombyx mori

scientific article

Characterization and functional investigation of an Arabidopsis cDNA encoding a homologue to the d-PGMase superfamily.

scientific article published on 28 February 2005

Characterization of the NAD+ binding site of Candida boidinii formate dehydrogenase by affinity labelling and site-directed mutagenesis

scientific article published on 01 November 2000

Characterization of the ligandin site of maize glutathione S-transferase I.

scientific article

Characterization of the relationship between integrase, excisionase and antirepressor activities associated with a superinfecting Shiga toxin encoding bacteriophage ⬇️

scientific article published on November 9, 2010

Comparative genomics of the anopheline glutathione S-transferase epsilon cluster

scientific article published in 2011

ConKit: a python interface to contact predictions

scientific article

Contemporary evolution of resistance at the major insecticide target site gene Ace-1 by mutation and copy number variation in the malaria mosquito Anopheles gambiae

scientific article published on 14 May 2015

Conversion of a disulfide bond into a thioacetal group during echinomycin biosynthesis

scientific article

Correction: Comparative Genomics of the Anopheline Glutathione S-Transferase Epsilon Cluster

Correction: Comparative Genomics of the Anopheline Glutathione S-Transferase Epsilon Cluster.

scientific article

Correction: Evaluating Caveolin Interactions: Do Proteins Interact with the Caveolin Scaffolding Domain through a Widespread Aromatic Residue-Rich Motif?

scientific article published on 25 February 2013

Corrigendum to: The protease inhibitor chagasin of Trypanosoma cruzi adopts an immunoglobulin-type fold and may have arisen by horizontal gene transfer (FEBS 25160)

article

Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions

scientific article published on 18 August 2018

Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain

scientific article

Design of new benzoxazole-2-thione-derived inhibitors of Streptococcus pneumoniae hyaluronan lyase: structure of a complex with a 2-phenylindole

scientific article published on 25 April 2006

Designed chimaeric galactosyl-mimodye ligands for the purification of Pseudomonas fluorescens beta-galactose dehydrogenase

scientific article published in March 2004

Deubiquitylases from genes to organism

scientific article published on July 2013

Distinct roles for Caf1, Ccr4, Edc3 and CutA in the co-ordination of transcript deadenylation, decapping and P-body formation in Aspergillus nidulans

scientific article published on 10 March 2010

Does distant homology with Evf reveal a lipid binding site in Bacillus thuringiensis cytolytic toxins?

scientific article published on 3 May 2009

Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1

scientific article (publication date: 2008)

Engineering the pH-dependence of kinetic parameters of maize glutathione S-transferase I by site-directed mutagenesis

scientific article published in April 2004

Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE.

scientific article published on 2 March 2018

Evaluating caveolin interactions: do proteins interact with the caveolin scaffolding domain through a widespread aromatic residue-rich motif?

scientific article

Evidence for loss of a partial flagellar glycolytic pathway during trypanosomatid evolution

scientific article

Evolutionary analysis of fructose 2,6-bisphosphate metabolism

scientific article

Exploration of pathomechanisms triggered by a single-nucleotide polymorphism in titin's I-band: the cardiomyopathy-linked mutation T2580I.

scientific article

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

scientific article

Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling

scientific article published on 25 February 2020

Extracellular calcium triggers unique transcriptional programs and modulates staurosporine-induced cell death in Neurospora crassa

scientific article published on 9 August 2014

Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors

scientific article

Ferric iron uptake genes are differentially expressed in the presence of copper sulfides in Acidithiobacillus ferrooxidans strain LR.

scientific article

Fold recognition analysis of glycosyltransferase families: further members of structural superfamilies

scientific article published on 24 July 2003

GP0.4 from bacteriophage T7: in silico characterisation of its structure and interaction with E. coli FtsZ

scientific article

Galactosyl-biomimetic dye-ligands for the purification of Dactylium dendroides galactose oxidase

scientific article

Galactosyl-mimodye ligands for Pseudomonas fluorescens beta-galactose dehydrogenase

scientific article published in November 2002

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

scientific article

Genome-based identification and characterization of a putative mucin-binding protein from the surface of Streptococcus pneumoniae.

scientific article

Genome-based identification of a carbohydrate binding module in Streptococcus pneumoniae hyaluronate lyase.

scientific article

Genome-wide association study of nevirapine hypersensitivity in a sub-Saharan African HIV-infected population

scientific article

Genome-wide transcriptional analyses in Anopheles mosquitoes reveal an unexpected association between salivary gland gene expression and insecticide resistance.

scientific article

Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes

scientific article

Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus

scientific article published on September 2017

Glycerol kinase of Trypanosoma brucei. Cloning, molecular characterization and mutagenesis.

scientific article published on April 2000

Helical ensembles outperform ideal helices in molecular replacement

scientific article published on 16 September 2020

Identification and analysis of catalytic TIM barrel domains in seven further glycoside hydrolase families

scientific article published in June 2003

Identification and modelling of a PPM protein phosphatase fold in the Legionella pneumophila deAMPylase SidD ⬇️

scientific article published on August 11, 2011

Identification of differentially expressed cDNA sequences in ovaries of sexual and apomictic plants of Brachiaria brizantha

scientific article published on December 2003

Identification of novel aspartic proteases from Strongyloides ratti and characterisation of their evolutionary relationships, stage-specific expression and molecular structure

scientific article

Identification, characterization and essentiality of the unusual peroxin 13 from Trypanosoma brucei.

scientific article

Implications of a genomic search for autophagy-related genes in trypanosomatids

article

Improving Cry8Ka toxin activity towards the cotton boll weevil (Anthonomus grandis)

scientific article

Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles

scientific article published on 06 February 2020

Inhibition of trypsin by cowpea thionin: Characterization, molecular modeling, and docking

scientific article published on 01 August 2002

Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling

scientific article (publication date: 9 May 2003)

Iterative database searches demonstrate that glycoside hydrolase families 27, 31, 36 and 66 share a common evolutionary origin with family 13.

scientific article published in July 2002

Jaburetox-2Ec: an insecticidal peptide derived from an isoform of urease from the plant Canavalia ensiformis

scientific article published on 17 August 2007

Kinetic characterization, structure modelling studies and crystallization of Trypanosoma brucei enolase

scientific article published on August 2003

L-Ascorbic acid 6-hexadecanoate, a potent hyaluronidase inhibitor. X-ray structure and molecular modeling of enzyme-inhibitor complexes

scientific article

Large scale ab initio modelling of structurally uncharacterized antimicrobial peptides reveals known and novel folds

scientific article published in February 2018

Leishmania donovani phosphofructokinase. Gene characterization, biochemical properties and structure-modeling studies

scientific article published in August 2002

Lpg0393 of Legionella pneumophila is a guanine-nucleotide exchange factor for Rab5, Rab21 and Rab22.

scientific article

Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation

scientific article

Maturation of the functional mouse CRES amyloid from globular form

scientific article published on 29 June 2020

Mechanistic and functional diversity in the mechanosensory kinases of the titin-like family

scientific article published on August 2013

Metabolic and target-site mechanisms combine to confer strong DDT resistance in Anopheles gambiae

scientific article published in 2014

Mining metagenomic data for novel domains: BACON, a new carbohydrate-binding module

scientific article

Molecular Dynamics and Electrochemical Investigations of a pH-Responsive Peptide Monolayer

Molecular basis for the fold organization and sarcomeric targeting of the muscle atrogin MuRF1

scientific article published on 26 March 2014

Molecular cloning of a cysteine proteinase cDNA from the cotton boll weevil Anthonomus grandis (Coleoptera: Curculionidae).

scientific article

Molecular cloning of alpha-amylases from cotton boll weevil, Anthonomus grandis and structural relations to plant inhibitors: an approach to insect resistance.

scientific article published in January 2003

Molecular modeling and inhibitory activity of cowpea cystatin against bean bruchid pests

scientific article published in May 2006

Molecular replacement using ab initio polyalanine models generated with ROSETTA.

scientific article published on 18 November 2008

Molecular replacement using structure predictions from databases

scientific article published on 19 November 2019

Monomorphic subtelomeric DNA in the filamentous fungus, Metarhizium anisopliae,contains a RecQ helicase-like gene

article

Mutagenic definition of a papain-like catalytic triad, sufficiency of the N-terminal domain for single-site core catalytic enzyme acylation, and C-terminal domain for augmentative metal activation of a eukaryotic phytochelatin synthase

scientific article published on 19 May 2006

New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins

scientific article

Novel compound heterozygous ASXL3 mutation causing Bainbridge-ropers like syndrome and primary IGF1 deficiency

scientific article published on 4 August 2017

Nucleotide sequence and phylogenetic analyses of the DNA polymerase gene of Anticarsia gemmatalis nucleopolyhedrovirus

scientific article

OMICS-Related Research in Latin America

scholarly article by Daniel J. Rigden published in June 2005

OMICS-Related Research in South America

scholarly article by Michael Y. Galperin published in March 2005

Order within a mosaic distribution of mitochondrial c-type cytochrome biogenesis systems?

scientific article published on 03 April 2008

Overlapping binding sites for trypsin and papain on a Kunitz-type proteinase inhibitor from Prosopis juliflora.

scientific article published in November 2002

Phosphoglycerate mutase from Schizosaccharomyces pombe: development of an expression system and characterisation of three histidine mutants of the enzyme

article

Plant alpha-amylase inhibitors and their interaction with insect alpha-amylases

scientific article

Plant-like traits associated with metabolism of Trypanosoma parasites

scientific article

Potential DNA binding and nuclease functions of ComEC domains characterized in silico

scientific article

Prediction of antimicrobial peptides based on the adaptive neuro-fuzzy inference system application

scientific article published in January 2012

PrfA protein of Bacillus species: prediction and demonstration of endonuclease activity on DNA

scientific article

Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics

scientific article published on 22 March 2017

Prophages encode phage-defense systems with cognate self-immunity

scientific article

Protein Phosphohistidine Phosphatases of the HP Superfamily

scientific article published on 01 January 2020

Purification, biochemical characterisation and partial primary structure of a new alpha-amylase inhibitor from Secale cereale (rye).

scientific article

RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis

scientific article published on 03 October 2020

Rab14 and its exchange factor FAM116 link endocytic recycling and adherens junction stability in migrating cells

scientific article

Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment.

scientific article published on 6 March 2018

Regulation of ecdysteroid signalling during Drosophila development: identification, characterization and modelling of ecdysone oxidase, an enzyme involved in control of ligand concentration

scientific article published on August 2005

Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds.

scientific article

Routine phasing of coiled-coil protein crystal structures with AMPLE

scientific article

SIMBAD: a sequence-independent molecular-replacement pipeline

scientific article published on 08 June 2018

Sequence analysis and characterization of a novel fibronectin-binding repeat domain from the surface of Streptococcus pneumoniae

scientific article

Sequence analysis of GerM and SpoVS, uncharacterized bacterial 'sporulation' proteins with widespread phylogenetic distribution

scientific article published on 17 June 2008

Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors

scientific article published in August 2002

Structural advances on titin: towards an atomic understanding of multi-domain functions in myofilament mechanics and scaffolding

scientific article

Structural annotation of the conserved carbohydrate esterase vb_24B_21 from Shiga toxin-encoding bacteriophage Φ24B

scientific article published on 03 August 2020

Structural diversity of calcium-binding proteins in bacteria: single-handed EF-hands?

scientific article published on 01 July 2003

Structural flexibility in Trypanosoma brucei enolase revealed by X-ray crystallography and molecular dynamics

scientific article

Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase

scientific article

Structural variability of the ubiquitin specific protease DUSP-UBL double domains

scientific article

Structure and function of Per-ARNT-Sim domains and their possible role in the life-cycle biology of Trypanosoma cruzi

scientific article

Structure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus with broad specificity phosphatase activity

scientific article

Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase

scientific article

Structure-activity studies on cysteine-substituted neurokinin A analogs

scientific article published on January 1999

Structures of Streptococcus pneumoniae hyaluronate lyase in complex with chondroitin and chondroitin sulfate disaccharides. Insights into specificity and mechanism of action

scientific article

Structures of phosphate and trivanadate complexes of Bacillus stearothermophilus phosphatase PhoE: structural and functional analysis in the cofactor-dependent phosphoglycerate mutase superfamily

scientific article

Sulphate ions observed in the 2.12 A structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism

scientific article

Systematic survey of deubiquitinase localization identifies USP21 as a regulator of centrosome- and microtubule-associated functions

scientific journal article

The 2.3 A X-ray crystal structure of S. cerevisiae phosphoglycerate mutase

scientific article

The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection

scientific article

The 2015 Nucleic Acids Research Database Issue and molecular biology database collection

scientific article

The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection

scientific article

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection

scientific article published on 18 December 2017

The 2021 Nucleic Acids Research database issue and the online molecular biology database collection

scientific article published on 01 January 2021

The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes

scientific article

The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes.

scientific article published in January 2017

The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection

scientific article published on 01 January 2019

The 27th annual Nucleic Acids Research database issue and molecular biology database collection

scientific article published on 01 January 2020

The <i>CCP</i>4 suite: integrative software for macromolecular crystallography

scientific article published in 2023

The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution

scientific article published in October 2004

The Glycosomal ATP‐Dependent Phosphofructokinase of Trypanosoma Brucei must have Evolved from an Ancestral Pyrophosphate‐Dependent Enzyme ⬇️

scientific article published on December 15, 1997

The PA14 domain, a conserved all-beta domain in bacterial toxins, enzymes, adhesins and signaling molecules

scientific article published in July 2004

The centrosomal deubiquitylase USP21 regulates Gli1 transcriptional activity and stability.

scientific article published on 12 September 2016

The crystal structure of Trypanosoma brucei enolase: visualisation of the inhibitory metal binding site III and potential as target for selective, irreversible inhibition

scientific article

The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold

scientific article

The heparin-binding proteome in normal pancreas and murine experimental acute pancreatitis.

scientific article published on 18 June 2019

The histidine phosphatase superfamily: structure and function

scientific article published on January 2008

The industrial melanism mutation in British peppered moths is a transposable element

scientific article

The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase.

scientific article published on 27 March 2007

The putative effector-binding site of Leishmania mexicana pyruvate kinase studied by site-directed mutagenesis

scientific article published on March 2002

The role of the C-terminal region in phosphoglycerate mutase.

scientific article published on January 1999

The structure of pyruvate kinase from Leishmania mexicana reveals details of the allosteric transition and unusual effector specificity

scientific article

The structure of the D49 phospholipase A2 piratoxin III from Bothrops pirajai reveals unprecedented structural displacement of the calcium-binding loop: possiblerelationship to cooperative substrate binding

scientific article (publication date: February 2003)

The structure-function relationship in the clostripain family of peptidases

scientific article published in March 2004

Titin kinase is an inactive pseudokinase scaffold that supports MuRF1 recruitment to the sarcomeric M-line ⬇️

scientific article

Transcriptomic analysis of Shiga-toxigenic bacteriophage carriage reveals a profound regulatory effect on acid resistance in Escherichia coli

scientific article published on 18 September 2015

Trypanosoma brucei contains a 2,3-bisphosphoglycerate independent phosphoglycerate mutase

scientific article

Trypanosomes contain two highly different isoforms of peroxin PEX13 involved in glycosome biogenesis

scientific article published on 26 May 2012

Ubiquitination of the glycosomal matrix protein receptor PEX5 in Trypanosoma brucei by PEX4 displays novel features.

scientific article published on 27 August 2013

Understanding the cell in terms of structure and function: insights from structural genomics.

scientific article

Unexpected catalytic site variation in phosphoprotein phosphatase homologues of cofactor-dependent phosphoglycerate mutase

scientific article published in February 2003

Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments

scientific article published in February 2002

Use of phage display to select novel cystatins specific for Acanthoscelides obtectus cysteine proteinases.

scientific article

Using Phaser and ensembles to improve the performance of SIMBAD

scientific article published on 01 January 2020

WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach

scientific article published on 01 April 2019

Weeds, worms, and more. Papain's long-lost cousin, phytochelatin synthase.

scientific article published in September 2004

m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome

scientific article published on 21 August 2020

m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human

scientific article published on 12 March 2020

mRNA 3' tagging is induced by nonsense-mediated decay and promotes ribosome dissociation.

scientific article published on 30 April 2012

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