Joan Planas-Iglesias
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View article: FireProtDB 2.0: large-scale manually curated database of the protein stability data
FireProtDB 2.0: large-scale manually curated database of the protein stability data Open
Thermostable proteins are crucial in numerous biomedical and biotechnological applications. However, naturally occurring proteins have evolved to function in mild conditions, and laboratory experiments aiming at improving protein stability…
View article: Kinetic mechanism of Renilla luciferase guides induced-fit engineering for improved bioluminescence
Kinetic mechanism of Renilla luciferase guides induced-fit engineering for improved bioluminescence Open
Renilla luciferase (RLuc) remains one of the most popular bioluminescence reporters, but its molecular principle has yet to be fully understood. Here, we reveal a detailed kinetic mechanism of the RLuc catalytic cycle which uncovers multip…
View article: Taurine Inhibits Apolipoprotein E4 Aggregation
Taurine Inhibits Apolipoprotein E4 Aggregation Open
Apolipoprotein E4 (ApoE4) is a major genetic risk factor in many neurodegenerative diseases, yet effective therapeutic strategies targeting its associated pathologies remain unresolved. The aggregation of ApoE4, a key pathological feature,…
View article: Automated Engineering Protein Dynamics via Loop Grafting: Improving <i>Renilla</i> Luciferase Catalysis
Automated Engineering Protein Dynamics via Loop Grafting: Improving <i>Renilla</i> Luciferase Catalysis Open
Engineering protein dynamics is a challenging and unsolved problem in protein design. Loop transplantation or loop grafting has been previously employed to transfer dynamic properties between proteins. We recently released a LoopGrafter We…
View article: Learning to engineer protein flexibility
Learning to engineer protein flexibility Open
Generative machine learning models are increasingly being used to design novel proteins for therapeutic and biotechnological applications. However, the current methods mostly focus on the design of proteins with a fixed backbone structure,…
View article: Analysis of mutations in precision oncology using the automated, accurate, and user-friendly web tool PredictONCO
Analysis of mutations in precision oncology using the automated, accurate, and user-friendly web tool PredictONCO Open
Next-generation sequencing technology has created many new opportunities for clinical diagnostics, but it faces the challenge of functional annotation of identified mutations. Various algorithms have been developed to predict the impact of…
View article: Visual Support for the Loop Grafting Workflow on Proteins
Visual Support for the Loop Grafting Workflow on Proteins Open
In understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on exploring regions in proteins called loops. Analyzing various characteristics of these regions helps the exper…
View article: A computational workflow for analysis of missense mutations in precision oncology
A computational workflow for analysis of missense mutations in precision oncology Open
Every year, more than 19 million cancer cases are diagnosed, and this number continues to increase annually. Since standard treatment options have varying success rates for different types of cancer, understanding the biology of an individ…
View article: Analysis of Mutations in Precision Oncology using The Automated, Accurate, and User-Friendly Web Tool PredictONCO
Analysis of Mutations in Precision Oncology using The Automated, Accurate, and User-Friendly Web Tool PredictONCO Open
Next-generation sequencing technology has created many new opportunities for clinical diagnostics, but it faces the challenge of functional annotation of identified mutations. Various algorithms have been developed to predict the impact of…
View article: A Computational Workflow for Analysis of Missense Mutations in Precision Oncology
A Computational Workflow for Analysis of Missense Mutations in Precision Oncology Open
Every year, more than 19 million cancer cases are diagnosed, and this number continues to increase annually. Since standard treatment options have varying success rates for different types of cancer, understanding the biology of an individ…
View article: CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules
CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules Open
Computational study of the effect of drug candidates on intrinsically disordered biomolecules is challenging due to their vast and complex conformational space. Here, we developed a comparative Markov state analysis (CoVAMPnet) framework t…
View article: AggreProt: a web server for predicting and engineering aggregation prone regions in proteins
AggreProt: a web server for predicting and engineering aggregation prone regions in proteins Open
Recombinant proteins play pivotal roles in numerous applications including industrial biocatalysts or therapeutics. Despite the recent progress in computational protein structure prediction, protein solubility and reduced aggregation prope…
View article: Deep Learning-Based Prediction and Suppression of Protein Aggregation- Prone Regions
Deep Learning-Based Prediction and Suppression of Protein Aggregation- Prone Regions Open
Identification of aggregation-prone regions in proteins and their suppression through mutations is a powerful strategy to enhance protein solubility and yield, significantly expanding their application potential. Here, we developed a deep …
View article: Training and test datasets for the PredictONCO tool
Training and test datasets for the PredictONCO tool Open
This dataset was used for training and validating the PredictONCO web tool, supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning. The dataset consists of …
View article: Training and test datasets for the PredictONCO tool
Training and test datasets for the PredictONCO tool Open
This dataset was used for training and validating the PredictONCO web tool, supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning. The dataset consists of …
View article: PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning
PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning Open
PredictONCO 1.0 is a unique web server that analyzes effects of mutations on proteins frequently altered in various cancer types. The server can assess the impact of mutations on the protein sequential and structural properties and apply a…
View article: Training and test datasets for the PredictONCO tool
Training and test datasets for the PredictONCO tool Open
This dataset was used for training and validating the PredictONCO web tool, supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning. The dataset consists of …
View article: SBILib: a handle for protein modeling and engineering
SBILib: a handle for protein modeling and engineering Open
Summary The SBILib Python library provides an integrated platform for the analysis of macromolecular structures and interactions. It combines simple 3D file parsing and workup methods with more advanced analytical tools. SBILib includes mo…
View article: Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer’s Disease drug candidate
Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer’s Disease drug candidate Open
View article: CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules
CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules Open
Computational study of the effect of drug candidates on intrinsically disordered biomolecules is challenging due to their vast and complex conformational space. Here we developed a Comparative Markov State Analysis (CoVAMPnet) framework to…
View article: Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry
Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry Open
View article: Domino-like Effect of C112R Mutation on ApoE4 Aggregation and Its Reduction by Alzheimer’s Disease Drug Candidate
Domino-like Effect of C112R Mutation on ApoE4 Aggregation and Its Reduction by Alzheimer’s Disease Drug Candidate Open
Background Apolipoprotein E (ApoE) ε4 genotype is the most prevalent risk factor for late-onset Alzheimer’s Disease (AD). Although ApoE4 differs from its non-pathological ApoE3 isoform only by the C112R mutation, the molecular mechanism of…
View article: LoopGrafter: a web tool for transplanting dynamical loops for protein engineering
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering Open
The transplantation of loops between structurally related proteins is a compelling method to improve the activity, specificity and stability of enzymes. However, despite the interest of loop regions in protein engineering, the available me…
View article: Characterization of the AGR2 Interactome Uncovers New Players of Protein Disulfide Isomerase Network in Cancer Cells
Characterization of the AGR2 Interactome Uncovers New Players of Protein Disulfide Isomerase Network in Cancer Cells Open
Anterior gradient 2 (AGR2) is an endoplasmic reticulum (ER)-resident protein disulfide isomerase (PDI) known to be overexpressed in many human epithelial cancers and is involved in cell migration, cellular transformation, angiogenesis, and…
View article: Engineering the protein dynamics of an ancestral luciferase
Engineering the protein dynamics of an ancestral luciferase Open
View article: Web-based tools for computational enzyme design
Web-based tools for computational enzyme design Open
View article: Computational Protein Stabilization Can Affect Folding Energy Landscapes and Lead to Domain-Swapped Dimers
Computational Protein Stabilization Can Affect Folding Energy Landscapes and Lead to Domain-Swapped Dimers Open
The functionality of a protein depends on its unique three-dimensional structure, which is a result of the folding process when the nascent polypeptide follows a funnel-like energy landscape to reach a global energy minimum. Computer-encod…
View article: Computational Protein Stabilization Can Affect Folding Energy Landscapes and Lead to Domain-Swapped Dimers
Computational Protein Stabilization Can Affect Folding Energy Landscapes and Lead to Domain-Swapped Dimers Open
The functionality of a protein depends on its unique three-dimensional structure, which is a result of the folding process when the nascent polypeptide follows a funnel-like energy landscape to reach a global energy minimum. Computer-encod…
View article: Web-based Tools for Computational Enzyme Design
Web-based Tools for Computational Enzyme Design Open
Enzymes are on high demand for very diverse biotechnological applications. However, natural biocatalysts often need to be engineered for fine-tuning their properties towards the end applications, such as the activity, selectivity, stabilit…
View article: Activity-dependent interdomain dynamics of matrix metalloprotease-1 on fibrin
Activity-dependent interdomain dynamics of matrix metalloprotease-1 on fibrin Open
The roles of protein conformational dynamics and allostery in function are well-known. However, the roles that interdomain dynamics have in function are not entirely understood. We used matrix metalloprotease-1 (MMP1) as a model system to …