Novel machine learning approaches revolutionize protein knowledge
Breakthrough methods in machine learning (ML), protein structure prediction, and novel
ultrafast structural aligners are revolutionizing structural biology. Obtaining accurate models …
ultrafast structural aligners are revolutionizing structural biology. Obtaining accurate models …
Accurate proteome-wide missense variant effect prediction with AlphaMissense
The vast majority of missense variants observed in the human genome are of unknown
clinical significance. We present AlphaMissense, an adaptation of AlphaFold fine-tuned on …
clinical significance. We present AlphaMissense, an adaptation of AlphaFold fine-tuned on …
Conformational ensembles of the human intrinsically disordered proteome
Intrinsically disordered proteins and regions (collectively, IDRs) are pervasive across
proteomes in all kingdoms of life, help to shape biological functions and are involved in …
proteomes in all kingdoms of life, help to shape biological functions and are involved in …
CADD v1. 7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions
M Schubach, T Maass, L Nazaretyan… - Nucleic acids …, 2024 - academic.oup.com
Abstract Machine Learning-based scoring and classification of genetic variants aids the
assessment of clinical findings and is employed to prioritize variants in diverse genetic …
assessment of clinical findings and is employed to prioritize variants in diverse genetic …
The power of computational proteomics platforms to decipher protein-protein interactions
M González-Avendaño, J López… - Current Opinion in …, 2024 - Elsevier
Adopting computational tools for analyzing extensive biological datasets has profoundly
transformed our understanding and interpretation of biological phenomena. Innovative …
transformed our understanding and interpretation of biological phenomena. Innovative …
Cross-protein transfer learning substantially improves disease variant prediction
Background Genetic variation in the human genome is a major determinant of individual
disease risk, but the vast majority of missense variants have unknown etiological effects …
disease risk, but the vast majority of missense variants have unknown etiological effects …
Conformational ensembles of the human intrinsically disordered proteome: Bridging chain compaction with function and sequence conservation
Intrinsically disordered proteins and regions (collectively IDRs) are pervasive across
proteomes in all kingdoms of life, help shape biological functions, and are involved in …
proteomes in all kingdoms of life, help shape biological functions, and are involved in …
Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per-and polyfluoroalkyl substance) biodegradation
HB Guo, VA Varaljay, G Kedziora, K Taylor… - Scientific Reports, 2023 - nature.com
Despite the success of AlphaFold2 (AF2), it is unclear how AF2 models accommodate for
ligand binding. Here, we start with a protein sequence from Acidimicrobiaceae TMED77 …
ligand binding. Here, we start with a protein sequence from Acidimicrobiaceae TMED77 …
Evaluating the use of paralogous protein domains to increase data availability for missense variant classification
AC Gunning, CF Wright - Genome Medicine, 2023 - Springer
Background Classification of rare missense variants remains an ongoing challenge in
genomic medicine. Evidence of pathogenicity is often sparse, and decisions about how to …
genomic medicine. Evidence of pathogenicity is often sparse, and decisions about how to …
Toward physics‐based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants
The goal of precision medicine is to utilize our knowledge of the molecular causes of
disease to better diagnose and treat patients. However, there is a substantial mismatch …
disease to better diagnose and treat patients. However, there is a substantial mismatch …