Bernard Offmann
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View article: Using protein blocks to build custom fragment libraries from protein structures
Using protein blocks to build custom fragment libraries from protein structures Open
The remarkable structural diversity of modern proteins reflects millions of years of evolution, during which sequence space has expanded while many structural features remain conserved. This conservation is evident not only among homologou…
View article: A 25-year journey with protein blocks: Unveiling the versatility of a structural alphabet
A 25-year journey with protein blocks: Unveiling the versatility of a structural alphabet Open
Protein Blocks (PBs) represent a widely used structural alphabet that enables the approximation and analysis of local protein conformations through 16 prototype fragments defined by dihedral angles. Initially developed to overcome the limi…
View article: Crystal structure of the sucrose phosphorylase from <i>Alteromonas mediterranea</i> shows a loop transition in the active site
Crystal structure of the sucrose phosphorylase from <i>Alteromonas mediterranea</i> shows a loop transition in the active site Open
Sucrose phosphorylases are essential enzymes regulating sucrose metabolism, and it has been shown that a loop rearrangement is essential to their catalytic cycle. Crystal structures of only six sucrose phosphorylase enzymes are available. …
View article: Sucrose phosphorylase from<i>Alteromonas mediterranea</i>: structural insight into the regioselective α-glucosylation of (+)-catechin
Sucrose phosphorylase from<i>Alteromonas mediterranea</i>: structural insight into the regioselective α-glucosylation of (+)-catechin Open
Sucrose phosphorylases, through transglycosylation reactions, are interesting enzymes that can transfer regioselectively glucose from sucrose, the donor substrate, onto acceptors like flavonoids to form glycoconjugates and hence modulate t…
View article: Enzymatic synthesis, characterization and molecular docking of a new functionalized polyphenol: Resveratrol-3,4′-⍺-diglucoside
Enzymatic synthesis, characterization and molecular docking of a new functionalized polyphenol: Resveratrol-3,4′-⍺-diglucoside Open
Transglucosylation of resveratrol by the Q345F variant of sucrose phosphorylase from Bifidobacterium adolescentis (BaSP) was extensively studied during the last decade. Indeed, Q345F is able to catalyze the synthesis of resveratrol-3-O-⍺-D…
View article: An Expanded Survey of the Moth PBP/GOBP Clade in Bombyx mori: New Insight into Expression and Functional Roles
An Expanded Survey of the Moth PBP/GOBP Clade in Bombyx mori: New Insight into Expression and Functional Roles Open
We studied the expression profile and ontogeny (from the egg stage through the larval stages and pupal stages, to the elderly adult age) of four OBPs from the silkworm moth Bombyx mori . We first showed that male responsiveness to female s…
View article: Docking of non-semiochemical ligands on silkworm Bombyx mori PBP1/GOBP2 binding sites
Docking of non-semiochemical ligands on silkworm Bombyx mori PBP1/GOBP2 binding sites Open
This work was mandatory on the basis of the following observations: age variations of PBP/GOBP expression independently of the male pheromone responsiveness, detection of PBP and GOBP proteins in aging female moths, PBP/GOBP expression in …
View article: Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction
Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction Open
The interaction between two proteins may involve local movements, such as small side-chains re-positioning or more global allosteric movements, such as domain rearrangement. We studied how one can build a precise and detailed protein-prote…
View article: Customised fragment libraries for ab initio protein structure prediction using a structural alphabet
Customised fragment libraries for ab initio protein structure prediction using a structural alphabet Open
Motivation: Computational protein structure prediction has taken over the structural community in past few decades, mostly focusing on the development of Template-Free modelling (TFM) or ab initio modelling protocols. Fragment-based assemb…
View article: Comprehensive History of CSP Genes: Evolution, Phylogenetic Distribution and Functions
Comprehensive History of CSP Genes: Evolution, Phylogenetic Distribution and Functions Open
In this review we present the developmental, histological, evolutionary and functional properties of insect chemosensory proteins (CSPs) in insect species. CSPs are small globular proteins folded like a prism and notoriously known for thei…
View article: A Machine Learning Approach for Efficient Selection of Enzyme Concentrations and Its Application for Flux Optimization
A Machine Learning Approach for Efficient Selection of Enzyme Concentrations and Its Application for Flux Optimization Open
The metabolic engineering of pathways has been used extensively to produce molecules of interest on an industrial scale. Methods like gene regulation or substrate channeling helped to improve the desired product yield. Cell-free systems ar…
View article: EcRBPome: a comprehensive database of all known E. coli RNA-binding proteins
EcRBPome: a comprehensive database of all known E. coli RNA-binding proteins Open
The repertoire of RNA-binding proteins (RBPs) in bacteria play a crucial role in their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. As a first step to…
View article: Flux prediction using artificial neural network (ANN) for the upper part of glycolysis
Flux prediction using artificial neural network (ANN) for the upper part of glycolysis Open
The selection of optimal enzyme concentration in multienzyme cascade reactions for the highest product yield in practice is very expensive and time-consuming process. The modelling of biological pathways is a difficult process because of t…
View article: PBmapclust: Mapping and Clustering the Protein Conformational Space Using a Structural Alphabet
PBmapclust: Mapping and Clustering the Protein Conformational Space Using a Structural Alphabet Open
Analyzing the data from molecular dynamics simulation of biological macromolecules like proteins is challenging. We propose a simple tool called PBmapclust that is based on a well established structural alphabet called Protein blocks (PB).…
View article: A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes
A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes Open
Directed evolution is an important research activity in synthetic biology and biotechnology. Numerous reports describe the application of tedious mutation/screening cycles for the improvement of proteins. Recently, knowledge-based approach…
View article: EcRBPome: a comprehensive database of all known <i>E. coli</i> RNA-binding proteins
EcRBPome: a comprehensive database of all known <i>E. coli</i> RNA-binding proteins Open
Background The repertoire of RNA-binding proteins (RBPs) in bacteria play crucial role for their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. As a fir…
View article: Knowledge-based prediction of protein backbone conformation using a structural alphabet
Knowledge-based prediction of protein backbone conformation using a structural alphabet Open
Libraries of structural prototypes that abstract protein local structures are known as structural alphabets and have proven to be very useful in various aspects of protein structure analyses and predictions. One such library, Protein Block…
View article: Genotyping and Bio-Sensing Chemosensory Proteins in Insects
Genotyping and Bio-Sensing Chemosensory Proteins in Insects Open
Genotyping is the process of determining differences in the genetic make-up of an individual and comparing it to that of another individual. Focus on the family of chemosensory proteins (CSPs) in insects reveals differences at the genomic …
View article: PB-kPRED: knowledge-based prediction of protein backbone conformation using a structural alphabet
PB-kPRED: knowledge-based prediction of protein backbone conformation using a structural alphabet Open
Libraries of structural prototypes that abstract protein local structures are known as structural alphabets and have proven to be very useful in various aspects of protein structure analyses and predictions. One such library, Protein Block…
View article: Biotype Characterization, Developmental Profiling, Insecticide Response and Binding Property of Bemisia tabaci Chemosensory Proteins: Role of CSP in Insect Defense
Biotype Characterization, Developmental Profiling, Insecticide Response and Binding Property of Bemisia tabaci Chemosensory Proteins: Role of CSP in Insect Defense Open
Chemosensory proteins (CSPs) are believed to play a key role in the chemosensory process in insects. Sequencing genomic DNA and RNA encoding CSP1, CSP2 and CSP3 in the sweet potato whitefly Bemisia tabaci showed strong variation between B …
View article: Modeling of a Cell-Free Synthetic System for Biohydrogen Production
Modeling of a Cell-Free Synthetic System for Biohydrogen Production Open
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