A5005706247- Protein Structure and Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Computational Drug Discovery Methods
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Enzyme Structure and Function
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- RNA and protein synthesis mechanisms
- Advanced Proteomics Techniques and Applications
- Genetic Associations and Epidemiology
- Sex and Gender in Healthcare
- SARS-CoV-2 and COVID-19 Research
- Computational Physics and Python Applications
- interferon and immune responses
- Animal Virus Infections Studies
- Microbial Community Ecology and Physiology
- CAR-T cell therapy research
- Cancer Immunotherapy and Biomarkers
- Genomics and Rare Diseases
- Single-cell and spatial transcriptomics
- RNA modifications and cancer
- Genetic Neurodegenerative Diseases
- Evolution and Genetic Dynamics
Barcelona Supercomputing Center
2020-2024
Josep Carreras Leukaemia Research Institute
2021-2024
Universitat Politècnica de Catalunya
2020-2024
European Commission
2024
Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of cell. Recent developments in computational methods for protein structure predictions have reached accuracy experimentally determined models. Although this has been independently verified, implementation these across structural-biology applications remains to be tested. Here, we evaluate use AlphaFold2 (AF2) study characteristic structural elements; impact missense variants;...
The protein structure field is experiencing a revolution. From the increased throughput of techniques to determine experimental structures, developments such as cryo-EM that allow us find structures large complexes or, more recently, development artificial intelligence tools, AlphaFold, can predict with high accuracy folding proteins for which availability homology templates limited. Here we quantify effect recently released AlphaFold database structural models in our knowledge on human...
Cancer driver events refer to key genetic aberrations that drive oncogenesis; however, their exact molecular mechanisms remain insufficiently understood. Here, our multi-omics pan-cancer analysis uncovers insights into the impacts of cancer drivers by identifying significant cis-effects and distal trans-effects quantified at RNA, protein, phosphoprotein levels. Salient observations include association point mutations copy-number alterations with rewiring protein interaction networks,...
Abstract Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of cell. Recent developments in computational methods have led to protein structure predictions reached accuracy experimentally determined models. While this has been independently verified, implementation these across structural biology applications remains be tested. Here, we evaluate use AlphaFold 2 (AF2) study characteristic elements; impact missense variants; ligand...
Abstract Energetic local frustration offers a biophysical perspective to interpret the effects of sequence variability on protein families. Here we present methodology analyze patterns within families and superfamilies that allows us uncover constraints related stability function, identify differential in with common ancestry. We these signals very well studied such as PDZ, SH3, ɑ β globins RAS Recent advances structure prediction make it possible vast majority space. An automatic...
Abstract According to the Principle of Minimal Frustration, folded proteins can only have a minimal number strong energetic conflicts in their native states. However, not all interactions are energetically optimized for folding but some remain conflict, i.e. they highly frustrated. This remaining local frustration has been shown be statistically correlated with distinct functional aspects such as protein-protein interaction sites, allosterism and catalysis. Fuelled by recent breakthroughs...
We present the results of assessment intramolecular residue-residue contact and distance predictions from groups participating in 14th round CASP experiment. The performance prediction methods was evaluated with measures used previous CASPs, while were assessed based on a new protocol, which considers individual pairs as well whole predicted matrix, using graph-based framework. evaluation indicate that by tFold framework, TripletRes DeepPotential most accurate both categories. With regards...
Abstract Energetic local frustration offers a biophysical perspective to interpret the effects of sequence variability on protein families. Here we present methodology analyze patterns within families that allows us uncover constraints related stability and function, identify differential in with common ancestry. We have analyzed these signals very well studied cases such as PDZ, SH3, α β globins RAS Recent advances structure prediction make it possible vast majority space. An automatic...
Abstract The protein structure field is experiencing a revolution. From the increased throughput of techniques to determine experimental structures, developments such as cryo-EM that allow us find structures large complexes or, more recently, development artificial intelligence tools, AlphaFold, can predict with high accuracy folding proteins for which availability homology templates limited. Here we quantify effect recently released AlphaFold database structural models in our knowledge on...
The recent emergence of the novel SARS-CoV-2 in China and its rapid spread human population has led to a public health crisis worldwide. Like SARS-CoV, horseshoe bats currently represent most likely candidate animal source for SARS-CoV-2. Yet, specific mechanisms cross-species transmission adaptation host remain unknown. Here we show that unsupervised analysis conservation patterns across β-CoV spike protein family, using sequence information alone, can provide valuable insights on molecular...
Precision medicine aims at tailoring treatments to individual patient needs. In this context, artificial intelligence (AI)-based technologies are viewed as revolutionary since they have the capacity identify key features that link genomic and phenotypic traits level. AI techniques therefore depend on quantity quality of data. When variables like sex, age, or race ignored in sample records, it can result biased predictions will not be considered training algorithm. To end, European...
The interpretation of genomic data is crucial to understand the molecular mechanisms biological processes. Protein structures play a vital role in facilitating this by providing functional context genetic coding variants. However, mapping genes proteins tedious and error-prone task due inconsistencies formats. Over past two decades, numerous tools databases have been developed automatically map annotated positions variants protein structures. most these are web-based not well-suited for...
Abstract Evolutionarily conserved protein-protein interactions (PPIs) reveal fundamental biological processes. However, predicting protein function solely from these provides an incomplete picture of systems. Computational methods for PPIs often struggle due to limited functional annotations in databases, making it difficult fully understand unique systems.. This study introduces ContextMirror2.0 (CM2.0), a coevolution-based method designed address limitations. Coevolutionary approaches,...
ABSTRACT The interpretation of genomic data is crucial to understand the molecular mechanisms biological processes. Protein structures play a vital role in facilitating this by providing functional context genetic coding variants. However, mapping genes proteins tedious and error-prone task due inconsistencies formats. Over past two decades, numerous tools databases have been developed automatically map annotated positions variants protein structures. most these are web-based not well-suited...
Abstract The recent emergence of the novel SARS-CoV-2 in China and its rapid spread human population has led to a public health crisis worldwide. Like SARS-CoV, horseshoe bats currently represent most likely candidate animal source for SARS-CoV-2. Yet, specific mechanisms cross-species transmission adaptation host remain unknown. Here we show that unsupervised analysis conservation patterns across β-CoV spike protein family, using sequence information alone, can provide rich on molecular...