Motivation: Proteins are known to undergo conformational changes in the course of their functions. The changes in conformation are often attributable to a small fraction of residues within the protein. Therefore identification of these variable regions is important for an understanding of protein function. Results: We …
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48 results for “Protein Identification”
Study improves LLMs for PPI analysis by addressing uncertainty.
problem Uncertainty in LLM predictions for PPIs.
method Fine-tuned LLaMA-3 and BioMedGPT models, LoRA ensembles, Bayesian LoRA for UQ.
result Competitive PPI identification performance across diverse disease contexts.
Study identifies cancer genes through graph anomaly analysis of protein interactions.
problem Insufficient modeling of biological information in protein interaction networks for cancer gene identification.
method Proposes HIerarchical-Perspective Graph Neural Network (HIPGNN) to detect weight heterogeneity and spectral flattening in cancer gene nodes.
result HIPGNN detects weight heterogeneity and spectral flattening, leading to improved cancer gene identification.
A new method predicts compounds for orphan proteins.
problem Predicting binding affinities for orphan proteins.
method Corresponding projections for transfer learning.
result The method outperforms state-of-the-art in orphan screening.
Improved peptide identification from mass spectrometry data.
problem Lack of large ground truth datasets for protein identification.
method Deep neural networks trained on imperfect hand-coded models.
result 43% improvement over standard matching methods.
The worldwide surge of multiresistant microbial strains has propelled the search for alternative treatment options. The study of Protein-Protein Interactions (PPIs) has been a cornerstone in the clarification of complex physiological and pathogenic processes, thus being a priority for the identification of vital compon…
ChemBoost predicts protein-ligand binding affinity using SMILES syntax.
problem Predicting high affinity drug-target interactions from sequence similarity alone.
method ChemBoost uses SMILES syntax to represent ligands as documents and proteins as sequences or ligand-centric features. It learns chemical word embeddings and predicts affinities using eXtreme Gradient Boosting.
result ChemBoost outperforms state-of-the-art systems in predicting protein-ligand affinities.
Improved protein identification in mass spectrometry data.
problem Expanding peptide scoring capabilities in tandem mass spectrometry.
method Deriving concave emission distributions for dynamic Bayesian networks.
result Efficiently learned scoring function outperforms state-of-the-art.
Identifying critical residues of a protein using meaningfully-thresholded Random Geometric Graphsq-bio.BM
Researchers identify critical protein residues using advanced graph theory.
problem Identifying essential residues in proteins for function.
method Learning Random Geometric Graphs (RGG) with Cramer's V correlation and organic thresholding.
result Advanced RGG methods accurately identify critical residues compared to existing techniques.
Generative model gradients enhance MS/MS peptide identification.
problem Improving peptide identification from MS/MS spectra.
method Leverage log-likelihood gradients of generative models in a kernel-based classifier.
result Fisher kernel outperforms other methods on MS/MS datasets.
Hierarchical, rotation-equivariant neural networks to select structural models of protein complexesq-bio.BM
New neural network predicts accurate protein complex structures.
problem Predicting accurate protein complex structures from atomic coordinates.
method Rotation-equivariant neural network combining point-based representation, equivariance, local convolutions, and hierarchical subsampling.
result Significant improvement in identifying accurate structural models.
NetBiTE predicts drug sensitivity and identifies biomarkers in cancer.
problem Predicting drug sensitivity and identifying biomarkers in cancer.
method NetBiTE combines prior knowledge and gene expression data using a biased tree ensemble approach.
result NetBiTE outperforms RF in predicting IC50 drug sensitivity for drugs targeting membrane receptor pathways.
Identification of feasible pathway information for c-di-GMP binding proteins in cellulose productionq-bio.QM
Paper uses machine learning to identify key pathways for c-di-GMP in bacterial genomes.
problem Understanding pathways essential for c-di-GMP in bacterial cellulose production.
method Applied Lasso and Random Forests for feature selection and modeling gene count data.
result Bacterial chemotaxis is identified as the most essential pathway for c-di-GMP encoding domains.
RNA-binding proteins (RBPs) play crucial roles in many biological processes, e.g. gene regulation. Computational identification of RBP binding sites on RNAs are urgently needed. In particular, RBPs bind to RNAs by recognizing sequence motifs. Thus, fast locating those motifs on RNA sequences is crucial and time-efficie…
Novel parallel GNN predicts protein-ligand interactions with high accuracy.
problem Accurate prediction of protein-ligand interactions for drug design.
method Parallel Graph Neural Networks (GNN) integrating 3D structural data.
result GNN achieves high accuracy in predicting binary interactions and activity.
Accelerating the identification of informative reduced representations of proteins with deep learning for graphsphysics.comp-ph
Deep learning speeds up protein mapping entropy calculation.
problem Efficiently calculating the mapping entropy of protein structures.
method Deep graph networks for accelerating mapping entropy computation.
result Deep graph networks achieve a speedup factor of up to 10^5.
Bayesian Semi-nonnegative Tri-matrix Factorization to Identify Pathways Associated with Cancer Typesstat.ML
Identifying altered pathways that are associated with specific cancer types can potentially bring a significant impact on cancer patient treatment. Accurate identification of such key altered pathways information can be used to develop novel therapeutic agents as well as to understand the molecular mechanisms of variou…
A novel methodology on distributed representations of proteins using their interacting ligandsstat.ML
The effective representation of proteins is a crucial task that directly affects the performance of many bioinformatics problems. Related proteins usually bind to similar ligands. Chemical characteristics of ligands are known to capture the functional and mechanistic properties of proteins suggesting that a ligand base…
A new framework uses text descriptions to improve protein design.
problem Lack of effective methods to incorporate textual descriptions in protein design.
method ProteinDT framework that combines text and protein structural information.
result ProteinDT significantly improves protein design accuracy and performance.
Paper presents a method for identifying isotope envelopes in MALDI-ToF data.
problem Deisotoping of isotopic peaks in MALDI-ToF molecular imaging data.
method Uses Mamdani-Assilan fuzzy system and spatial maps of molecular distribution to identify isotope envelopes.
result Proposed method detects overlapping envelopes and analyzes large data sets.
Deep learning models optimize protein sequences.
problem Optimizing protein properties through sequence design.
method Deep generative models guided by machine learning.
result Improved protein sequence generation from prior knowledge.
The identification of novel drug-target (DT) interactions is a substantial part of the drug discovery process. Most of the computational methods that have been proposed to predict DT interactions have focused on binary classification, where the goal is to determine whether a DT pair interacts or not. However, protein-l…
Mathematical pipeline identifies structural homology of knotted proteins.
problem Quantification and classification of protein structures, especially knotted proteins, require noise-free and complete data.
method Developed a geometric framework using persistent homology to analyze protein structures.
result Persistent homology accurately represents structural homology of knotted proteins and identifies geometric features of protein entanglement.
PLIT identifies plant lncRNAs from RNA-seq data with high accuracy.
problem Inaccurate identification of lncRNAs in plant transcriptomic datasets.
method PLIT uses L1 regularization and iRF classification to select optimal features from sequence and codon-bias data.
result PLIT outperforms existing CPC tools in identifying lncRNAs in plant RNA-seq datasets.
ProGen models protein sequences for synthetic biology.
problem Generating proteins without structural annotations.
method Trained a 1.2B-parameter language model on 280M protein sequences.
result ProGen generates proteins with fine-grained control and accuracy.
Parallel Protein Community Detection in Large-scale PPI Networks Based on Multi-source Learningcs.SI
Paper proposes MLPCD for protein community detection in large PPI networks.
problem Identifying reliable protein communities from large-scale PPI networks.
method Integrates Gene Expression Data and uses Multi-source Learning with cloud computing.
result Demonstrates superior performance compared to existing methods.
New 3D protein analysis methods improve accuracy.
problem Lack of suitable learning algorithms for protein data.
method Intrinsic-Extrinsic Convolution and Pooling for 3D protein structures.
result Outperforms state-of-the-art methods on protein analysis tasks.
New method detects and compares folding pathways of knotted proteins.
problem Understanding the function of knots in protein folding.
method Topological analysis of protein knotoid distributions and entanglement.
result Reveals unique folding pathway for shallow knotted Carbonic Anhydrases.
Proteins are commonly used by biochemical industry for numerous processes. Refining these proteins' properties via mutations causes stability effects as well. Accurate computational method to predict how mutations affect protein stability are necessary to facilitate efficient protein design. However, accuracy of predic…
Improved protein structure classification using weighted graphlets and deep neural networks.
problem Protein structure classification for function prediction.
method Developed a weighted network and graphlet-based measure, combined with a deep neural network.
result Significantly improved performance on 36 real datasets compared to existing methods.
PANDA: Predicting the change in proteins binding affinity upon mutations using sequence informationq-bio.BM
PANDA predicts protein binding affinity changes from sequences, outperforming existing methods.
problem Accurately predicting changes in protein binding affinity due to mutations.
method Sequence-based machine learning approach using protein sequence information.
result PANDA achieves higher Pearson correlation coefficients than existing methods.
A Novel Mathematical Model of Protein Interactions from the Perspective of Electron Delocalizationq-bio.BM
A new model explains protein interactions via electron delocalization.
problem Understanding how protein interactions affect each other.
method Quantized discrete differential geometry of n-simplices.
result Allosteric regulation follows from the model of interactions.
EBM predicts protein conformations at atomic scale using crystallized data.
problem Predicting the conformation of a side chain from its context within a protein structure.
method Energy-based model trained on crystallized protein data, evaluating performance on rotamer recovery task.
result EBM achieves performance close to state-of-the-art methods, including Rosetta energy function.
Knot theory applied to proteins, distinguishing folded linear chains.
problem Classifying proteins as unknots when intra-chain interactions are ignored.
method Developing knot theory for folded linear molecular chains, considering self-bonding, and using Gauss codes and quandles.
result Extended knot theory to distinguish topologies of proteins with intra-chain bonds.
Improving Estimation of the Koopman Operator with Kolmogorov-Smirnov Indicator Functionsphysics.data-an
The paper proposes a method to improve Koopman operator estimation using indicator functions.
problem Difficulty in identifying good observables for Koopman operator expansion.
method Clustering procedure based on Hidden Markov Model (HMM) to infer surrogate observables.
result Inferred indicator functions significantly improve estimation of Koopman operator eigenvalues and transition timescales.
Experimental determination of protein function is resource-consuming. As an alternative, computational prediction of protein function has received attention. In this context, protein structural classification (PSC) can help, by allowing for determining structural classes of currently unclassified proteins based on thei…
Machine learning identifies key metabolic control circuits in bacterial pathways.
problem Identifying regulated metabolic pathways in bacteria.
method Machine learning approach analyzing multi-omics data.
result Identification of E. coli Glycolysis regulatory circuits.
Mathematician summarizes protein geometry and mutation effects.
problem Understanding how proteins mutate and their structure-function relationship.
method Mathematical analysis of protein structures and functions, focusing on hydrogen bonds and secondary structure.
result Protein secondary structure regulates mutation by stabilizing or destabilizing regions.
Machine learning for protein folding and dynamicsphysics.bio-ph
Machine learning predicts protein structures and simulates dynamics.
problem Understanding and predicting protein folding and dynamics.
method Machine learning techniques for structure prediction and simulation.
result Machine learning enhances protein simulation and structure prediction.
A new method predicts protein functions using variable-length sequences.
problem Computational methods for protein function prediction are slow and inaccurate for long sequences.
method Two feature sets: single fixed-sized segments and multi-sized segments, using bi-directional LSTM. Combined with MLDA features.
result Significant improvement in accuracy for long protein sequences.
EGR refines and assesses protein complex structures.
problem Improving the accuracy of protein complex 3D structures for drug discovery.
method E(3)-equivariant graph neural network (GNN) for multi-task refinement and assessment.
result EGR achieves state-of-the-art performance in refining and assessing protein complexes.
Fatgraph Models of Proteinsq-bio.BM
We introduce a new model of proteins, which extends and enhances the traditional graphical representation by associating a combinatorial object called a fatgraph to any protein based upon its intrinsic geometry. Fatgraphs can easily be stored and manipulated as triples of permutations, and these methods are therefore a…
ProteinNet provides a standardized data set for protein structure prediction.
problem Lack of standardized data sets for protein structure prediction.
method Created high-quality sequence alignments, multiple data splits, and validation sets.
result Facilitates fair assessment of machine learning models for protein structure.
Two proteins are homologous if they have a common evolutionary origin, and the binary classification problem is to identify proteins in a candidate set that are homologous to a particular native protein. The feature (explanatory) variables available for classification are various measures of similarity of proteins. The…
Flexible Kernels for Protein Property Prediction
problem Predicting protein properties from sparse experimental data
method Sequence kernels using evolutionary substitution matrices and local linearity
result Data-efficient models of protein property landscapes
New method maps protein sequences to embeddings encoding structural information.
problem Inferring structural properties from amino acid sequences when structures are unknown.
method Representation learning using bidirectional LSTM models with structural similarity and residue contact maps.
result Trained embeddings improve structural similarity prediction and transfer to other tasks.
New method steers protein design towards desired properties.
problem Challenges in designing proteins with specific structures and properties.
method Feynman-Kac framework applied to RFdiffusion models with guiding potentials.
result Significant improvement in predicted interface energetics and binder designability.
A new diffusion model generates novel protein backbones without relying on pretrained networks.
problem Generating novel protein backbones without relying on pretrained networks.
method Developed a SE(3) invariant diffusion model on multiple frames, called FrameDiff.
result Generated designable protein monomers up to 500 amino acids without pretrained networks.