73 hasil untuk "Burkhard Rost"
Menampilkan 1–20 · 0,80 detik · RSS
-
Artikel Jurnal
SETH predicts nuances of residue disorder from protein embeddings
Predictions for millions of protein three-dimensional structures are only a few clicks away since the release of AlphaFold2 results for UniProt. However, many proteins have so-called intrinsically disordered regions (IDRs) that do not adopt unique structures in isolation. These IDRs are associated…
-
Artikel Jurnal Teks lengkap
Protein-protein interaction hotspots carved into sequences.
Protein-protein interactions, a key to almost any biological process, are mediated by molecular mechanisms that are not entirely clear. The study of these mechanisms often focuses on all residues at protein-protein interfaces. However, only a small subset of all interface residues is actually…
Juga tersedia di: PLOS
-
Artikel Jurnal Teks lengkap
Alternative protein-protein interfaces are frequent exceptions.
The intricate molecular details of protein-protein interactions (PPIs) are crucial for function. Therefore, measuring the same interacting protein pair again, we expect the same result. This work measured the similarity in the molecular details of interaction for the same and for homologous protein…
Juga tersedia di: PLOS
-
Artikel Jurnal Teks lengkap
Protein-protein interactions more conserved within species than across species.
Experimental high-throughput studies of protein-protein interactions are beginning to provide enough data for comprehensive computational studies. Today, about ten large data sets, each with thousands of interacting pairs, coarsely sample the interactions in fly, human, worm, and yeast. Another…
Juga tersedia di: PLOS
-
Artikel Jurnal
TMbed: transmembrane proteins predicted through language model embeddings
Abstract Background Despite the immense importance of transmembrane proteins (TMP) for molecular biology and medicine, experimental 3D structures for TMPs remain about 4–5 times underrepresented compared to non-TMPs. Today’s top methods such as AlphaFold2 accurately predict 3D structures for many…
-
Artikel Jurnal
Assessing the role of evolutionary information for enhancing protein language model embeddings
Abstract Embeddings from protein Language Models (pLMs) are replacing evolutionary information from multiple sequence alignments (MSAs) as the most successful input for protein prediction. Is this because embeddings capture evolutionary information? We tested various approaches to explicitly…
-
Artikel Jurnal
Rendering protein mutation movies with MutAmore
Abstract Background The success of AlphaFold2 in reliable protein three-dimensional (3D) structure prediction, assists the move of structural biology toward studies of protein dynamics and mutational impact on structure and function. This transition needs tools that qualitatively assess alternative…
-
Artikel Jurnal
Nearest neighbor search on embeddings rapidly identifies distant protein relations
Since 1992, all state-of-the-art methods for fast and sensitive identification of evolutionary, structural, and functional relations between proteins (also referred to as “homology detection”) use sequences and sequence-profiles (PSSMs). Protein Language Models (pLMs) generalize sequences, possibly…
-
Artikel Jurnal Teks lengkap
Natively unstructured loops differ from other loops.
Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered…
-
Artikel Jurnal Teks lengkap
Accelerating the Original Profile Kernel.
One of the most accurate multi-class protein classification systems continues to be the profile-based SVM kernel introduced by the Leslie group. Unfortunately, its CPU requirements render it too slow for practical applications of large-scale classification tasks. Here, we introduce several software…
-
Artikel Jurnal Teks lengkap
Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes.
Many prokaryotic organisms have adapted to incredibly extreme habitats. The genomes of such extremophiles differ from their non-extremophile relatives. For example, some proteins in thermophiles sustain high temperatures by being more compact than homologs in non-extremophiles. Conversely, some…
-
Artikel Jurnal
Protein–protein and protein-nucleic acid binding residues important for common and rare sequence variants in human
Abstract Background Any two unrelated people differ by about 20,000 missense mutations (also referred to as SAVs: Single Amino acid Variants or missense SNV). Many SAVs have been predicted to strongly affect molecular protein function. Common SAVs (> 5% of population) were predicted to have, on…
-
Artikel Jurnal Teks lengkap
Distinguishing protein-coding from non-coding RNAs through support vector machines.
RIKEN's FANTOM project has revealed many previously unknown coding sequences, as well as an unexpected degree of variation in transcripts resulting from alternative promoter usage and splicing. Ever more transcripts that do not code for proteins have been identified by transcriptome studies, in…
-
Artikel Jurnal
Variant effect predictions capture some aspects of deep mutational scanning experiments
Abstract Background Deep mutational scanning (DMS) studies exploit the mutational landscape of sequence variation by systematically and comprehensively assaying the effect of single amino acid variants (SAVs; also referred to as missense mutations, or non-synonymous Single Nucleotide Variants –…
-
Artikel Jurnal
bindNode24: Competitive binding residue prediction with 60 % smaller model
Many proteins function through ligand binding. Yet, reliable experimental binding data remains limited. Recent advances predict binding residues from sequences using protein Language Model embeddings. The AlphaFold Protein Structure Database, which has reliable 3D structure predictions from…
-
Artikel Jurnal
ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes.
MotivationProtein-protein interactions (PPIs) play a key role in many cellular processes. Most annotations of PPIs mix experimental and computational data. The mix optimizes coverage, but obfuscates the annotation origin. Some resources excel at focusing on reliable experimental data. Here, we…
-
Artikel Jurnal
Fine-tuning protein language models boosts predictions across diverse tasks
Abstract Prediction methods inputting embeddings from protein language models have reached or even surpassed state-of-the-art performance on many protein prediction tasks. In natural language processing fine-tuning large language models has become the de facto standard. In contrast, most protein…