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Mismatch string kernels for discriminative protein classification

https://doi.org/10.1093/bioinformatics/btg431

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Embedding strategies for effective use of information from multiple sequence alignments

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What is the value added by human intervention in protein structure prediction?

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Hidden Markov Models in Computational Biology

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Fast Kernels for Inexact String Matching

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SCOP: A structural classification of proteins database for the investigation of sequences and structures

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Basic Local Alignment Search Tool

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An Efficient Extension to Mixture Techniques for Prediction and Decision Trees

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Profile analysis: detection of distantly related proteins.

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Hidden Markov models of biological primary sequence information.

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A Discriminative Framework for Detecting Remote Protein Homologies

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A Novel Approach to Remote Homology Detection: Jumping Alignments

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Protein Family Classification Using Sparse Markov Transducers

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Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships

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An algorithm for finding signals of unknown length in DNA sequences

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The PROSITE database, its status in 1995

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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The PRINTS protein fingerprint database in its fifth year

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The ASTRAL compendium for protein structure and sequence analysis

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Phylogenetic analysis Of Dna sequences

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THE SPECTRUM KERNEL: A STRING KERNEL FOR SVM PROTEIN CLASSIFICATION

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A training algorithm for optimal margin classifiers

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An efficient extension to mixture techniques for prediction and decision trees

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Combining pairwise sequence similarity and support vector machines for remote protein homology detection

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A New Discriminative Kernel from Probabilistic Models

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Statistical Learning Theory

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Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology

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Dynamic Alignment Kernels

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Fast Kernels for String and Tree Matching

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Detecting Remote Protein Evolutionary Relationships Via String Scoring Method

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Using Fuzzy Equivalence Relations to Model Position Specificity in Sequence Kernels

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String Kernels of Imperfect Matches for Off-target Detection in RNA Interference

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A Class of New Kernels Based on High-Scored Pairs of k-Peptides for SVMs and Its Application for Prediction of Protein Subcellular Localization

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Human Papillomavirus Risk Type Classification from Protein Sequences Using Support Vector Machines

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Structural relatedness via flow networks in protein sequence space

inferred← citeshttps://doi.org/10.1016/j.jtbi.2010.06.006openalex-snapshot

High performance set of PseAAC and sequence based descriptors for protein classification

inferred← citeshttps://doi.org/10.1016/j.jtbi.2013.08.037openalex-snapshot

Predicting anticancer peptides with Chou′s pseudo amino acid composition and investigating their mutagenicity via Ames test

inferred← citeshttps://doi.org/10.1016/j.jtbi.2016.05.011openalex-snapshot

Machine learning approaches for discrimination of Extracellular Matrix proteins using hybrid feature space

inferred← citeshttps://doi.org/10.1016/j.neucom.2009.12.038openalex-snapshot

Classifying proteins using gapped Markov feature pairs

inferred← citeshttps://doi.org/10.1016/j.neucom.2016.03.079openalex-snapshot

Multi-fields model for predicting target–ligand interaction

inferred← citeshttps://doi.org/10.1016/j.neunet.2005.07.002openalex-snapshot

A novel approach to extracting features from motif content and protein composition for protein sequence classification

inferred← citeshttps://doi.org/10.1016/j.neunet.2005.07.004openalex-snapshot

Special issue on neural networks and kernel methods for structured domains

inferred← citeshttps://doi.org/10.1016/j.neunet.2008.08.002openalex-snapshot

LAGO on the unit sphere

inferred← citeshttps://doi.org/10.1016/j.omtn.2019.07.019openalex-snapshot

Selecting Essential MicroRNAs Using a Novel Voting Method

inferred← citeshttps://doi.org/10.1016/j.patcog.2005.11.012openalex-snapshot

Classifying protein sequences using hydropathy blocks

inferred← citeshttps://doi.org/10.1016/j.patcog.2009.12.008openalex-snapshot

Learning state machine-based string edit kernels

inferred← citeshttps://doi.org/10.1016/j.patcog.2010.11.020openalex-snapshot

A sum-over-paths extension of edit distances accounting for all sequence alignments

inferred← citeshttps://doi.org/10.1016/j.patrec.2010.05.004openalex-snapshot

A composite kernel for named entity recognition

inferred← citeshttps://doi.org/10.1016/j.sbi.2006.05.006openalex-snapshot

Sequence comparison and protein structure prediction

inferred← citeshttps://doi.org/10.1016/j.tcs.2005.08.026openalex-snapshot

From Hopfield nets to recursive networks to graph machines: Numerical machine learning for structured data

inferred← citeshttps://doi.org/10.1016/j.theriogenology.2011.12.011openalex-snapshot

Taking advantage of the use of supervised learning methods for characterization of sperm population structure related with freezability in the Iberian red deer

inferred← citeshttps://doi.org/10.1016/j.ultsonch.2019.03.031openalex-snapshot

Classification and prediction of inertial cavitation activity induced by pulsed high-intensity focused ultrasound

inferred← citeshttps://doi.org/10.1016/j.ymeth.2019.07.013openalex-snapshot

CRISPR-Cas bioinformatics

inferred← citeshttps://doi.org/10.1016/s1574-1400(08)00003-0openalex-snapshot

Machine Learning for Protein Structure and Function Prediction

inferred← citeshttps://doi.org/10.1016/s1672-0229(08)60027-3openalex-snapshot

Identification of MicroRNA Precursors with Support Vector Machine and String Kernel

inferred← citeshttps://doi.org/10.1021/acs.langmuir.4c00543openalex-snapshot

Intelligent Design of Antithrombotic Peptide Targeting Collagen

inferred← citeshttps://doi.org/10.1021/ci1001394openalex-snapshot

Cross-Target View to Feature Selection: Identification of Molecular Interaction Features in Ligand−Target Space

inferred← citeshttps://doi.org/10.1021/ci200278wopenalex-snapshot

String Kernels and High-Quality Data Set for Improved Prediction of Kinked Helices in α-Helical Membrane Proteins

inferred← citeshttps://doi.org/10.1021/ci300515zopenalex-snapshot

Chemical Genomics Approach for GPCR–Ligand Interaction Prediction and Extraction of Ligand Binding Determinants

inferred← citeshttps://doi.org/10.1021/ci600397popenalex-snapshot

One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties

inferred← citeshttps://doi.org/10.1038/msb.2011.5openalex-snapshot

Analysis of multiple compound–protein interactions reveals novel bioactive molecules

inferred← citeshttps://doi.org/10.1038/npre.2010.4708.1openalex-snapshot

Decoding Sequence Classification Models for Acquiring New Biological Insights

inferred← citeshttps://doi.org/10.1038/s41592-019-0496-6openalex-snapshot

Machine-learning-guided directed evolution for protein engineering

inferred← citeshttps://doi.org/10.1038/s41598-020-80786-0openalex-snapshot

Embeddings from deep learning transfer GO annotations beyond homology

inferred← citeshttps://doi.org/10.1038/s42256-022-00553-wopenalex-snapshot

Predicting unseen antibodies’ neutralizability via adaptive graph neural networks

inferred← citeshttps://doi.org/10.1038/srep23934openalex-snapshot

Recombination spot identification Based on gapped k-mers

inferred← citeshttps://doi.org/10.1039/d0sm01644fopenalex-snapshot

In search of a novel chassis material for synthetic cells: emergence of synthetic peptide compartment

inferred← citeshttps://doi.org/10.1039/d2me00169aopenalex-snapshot

Computational design of self-assembling peptide chassis materials for synthetic cells

inferred← citeshttps://doi.org/10.1073/pnas.0505411102openalex-snapshot

Framework for kernel regularization with application to protein clustering

inferred← citeshttps://doi.org/10.1073/pnas.0906801106openalex-snapshot

Proteome-wide prediction of acetylation substrates

inferred← citeshttps://doi.org/10.1073/pnas.1816640116openalex-snapshot

Repertoires of G protein-coupled receptors for Ciona -specific neuropeptides

inferred← citeshttps://doi.org/10.1074/mcp.m110.004994openalex-snapshot

Complex Networks Govern Coiled-Coil Oligomerization – Predicting and Profiling by Means of a Machine Learning Approach

inferred← citeshttps://doi.org/10.1080/00949655.2023.2266084openalex-snapshot

A Cox-optimized survival model based on GrowNet

inferred← citeshttps://doi.org/10.1080/02331934.2011.611515openalex-snapshot

New SDP models for protein homology detection with semi-supervised SVM

inferred← citeshttps://doi.org/10.1080/07391102.2007.10507177openalex-snapshot

Using Recurrence Quantification Analysis Descriptors for Protein Sequence Classification with Support Vector Machines

inferred← citeshttps://doi.org/10.1088/1742-6596/1108/1/012052openalex-snapshot

Fuzzy Support Vector Machines based on Adaptive Particle Swarm Optimization for Credit Risk Analysis

inferred← citeshttps://doi.org/10.1089/cmb.2008.0147openalex-snapshot

Applying Fuzzy Technologies to Equivalence Learning in Protein Classification

inferred← citeshttps://doi.org/10.1089/cmb.2010.0171openalex-snapshot

The Irredundant Class Method for Remote Homology Detection of Protein Sequences

inferred← citeshttps://doi.org/10.1089/cmb.2014.0173openalex-snapshot

A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and k -Mer Distances

inferred← citeshttps://doi.org/10.1093/bfgp/elad007openalex-snapshot

ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning

inferred← citeshttps://doi.org/10.1093/bib/5.4.328openalex-snapshot

Biological applications of support vector machines

inferred← citeshttps://doi.org/10.1093/bib/bbad156openalex-snapshot

A survey on algorithms to characterize transcription factor binding sites

inferred← citeshttps://doi.org/10.1093/bib/bbm064openalex-snapshot

ROC analysis: applications to the classification of biological sequences and 3D structures

inferred← citeshttps://doi.org/10.1093/bib/bbn027openalex-snapshot

Penalized feature selection and classification in bioinformatics

inferred← citeshttps://doi.org/10.1093/bib/bbw108openalex-snapshot

A comprehensive review and comparison of different computational methods for protein remote homology detection

inferred← citeshttps://doi.org/10.1093/bib/bbx165openalex-snapshot

BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches

inferred← citeshttps://doi.org/10.1093/bib/bbz101openalex-snapshot

Flexible k-mers with variable-length indels for identifying binding sequences of protein dimers

inferred← citeshttps://doi.org/10.1093/bioinformatics/btac155openalex-snapshot

BridgeDPI: a novel Graph Neural Network for predicting drug–protein interactions

inferred← citeshttps://doi.org/10.1093/bioinformatics/bti1024openalex-snapshot

Classifying noisy protein sequence data: a case study of immunoglobulin light chains

inferred← citeshttps://doi.org/10.1093/bioinformatics/bti1055openalex-snapshot

Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity

inferred← citeshttps://doi.org/10.1093/bioinformatics/bti132openalex-snapshot

Accurate identification of alternatively spliced exons using support vector machine

inferred← citeshttps://doi.org/10.1093/bioinformatics/bti608openalex-snapshot

Motif-based protein ranking by network propagation

inferred← citeshttps://doi.org/10.1093/bioinformatics/bti771openalex-snapshot

Improved prediction of bacterial transcription start sites

showing the first 200 of 514

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