A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

No abstract is available for this paper.

• Publication year

  2015

• Venue

  IEEE/ACM Transactions on Computational Biology & Bioinformatics

• Publication date

  Unknown publication date

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1109/TCBB.2014.2343960PMID 25750595PMCID PMC4348072
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Critical assessment of methods of protein structure prediction (CASP) — round x

  2014cited by this paper
• Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction

  2014cited by this paper
• DNdisorder: predicting protein disorder using boosting and deep networks

  2013cited by this paper
• Template-based protein structure modeling using the RaptorX web server

  2012cited by this paper
• Deep architectures for protein contact map prediction

  2012cited by this paper
• Predicting protein residue-residue contacts using deep networks and boosting

  2012cited by this paper
• ESpritz: accurate and fast prediction of protein disorder

  2012cited by this paper
• A Unified Multitask Architecture for Predicting Local Protein Properties

  2012cited by this paper
• SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles

  2012cited by this paper
• A Practical Guide to Training Restricted Boltzmann Machines

  2012cited by this paper
• Critical assessment of methods of protein structure prediction (CASP)—round IX

  2011cited by this paper
• Improving protein secondary structure prediction based on short subsequences with local structure similarity

  2010cited by this paper
• A series of PDB related databases for everyday needs

  2010cited by this paper
• Protein 8-class secondary structure prediction using Conditional Neural Fields

  2010influential reference
• CUDAMat: a CUDA-based matrix class for Python

  2009cited by this paper
• REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform

  2009cited by this paper
• The Jpred 3 secondary structure prediction server

  2008cited by this paper
• A dynamic Bayesian network approach to protein secondary structure prediction

  2008cited by this paper
• Achieving 80% ten‐fold cross‐validated accuracy for secondary structure prediction by large‐scale training

  2006cited by this paper
• Protein secondary structure prediction for a single-sequence using hidden semi-Markov models

  2006cited by this paper
• A Fast Learning Algorithm for Deep Belief Nets

  2006cited by this paper
• Supporting Online Material for Reducing the Dimensionality of Data with Neural Networks

  2006cited by this paper
• Advances in protein structure prediction and de novo protein design : A review

  2006influential reference
• Porter: a new, accurate server for protein secondary structure prediction

  2005cited by this paper
• SCRATCH: a protein structure and structural feature prediction server

  2005influential reference
• Solving the protein sequence metric problem.

  2005influential reference
• A novel method for protein secondary structure prediction using dual‐layer SVM and profiles

  2004cited by this paper
• Improving fold recognition without folds.

  2004cited by this paper
• Automated protein structure homology modeling: a progress report.

  2004cited by this paper
• Critical assessment of methods of protein structure prediction (CASP)‐round V

  2003cited by this paper
• Protein secondary structure prediction based on an improved support vector machines approach.

  2003influential reference
• Secondary structure prediction with support vector machines

  2003cited by this paper
• Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles

  2002cited by this paper
• Training Products of Experts by Minimizing Contrastive Divergence

  2002cited by this paper
• A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach.

  2001cited by this paper
• Assessment of novel fold targets in CASP4: Predictions of three‐dimensional structures, secondary structures, and interresidue contacts

  2001cited by this paper
• Generation and evaluation of dimension-reduced amino acid parameter representations by artificial neural networks

  2001cited by this paper
• Application of multiple sequence alignment profiles to improve protein secondary structure prediction

  2000cited by this paper
• The Protein Data Bank

  2000cited by this paper
• The PSIPRED protein structure prediction server

  2000influential reference
• Prediction of protein secondary structure at 80% accuracy

  2000cited by this paper
• A modified definition of Sov, a segment‐based measure for protein secondary structure prediction assessment

  1999cited by this paper
• Protein secondary structure prediction based on position-specific scoring matrices.

  1999influential reference
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997cited by this paper
• Neural network-based face detection

  1996cited by this paper
• GOR method for predicting protein secondary structure from amino acid sequence.

  1996cited by this paper
• Combining evolutionary information and neural networks to predict protein secondary structure

  1994cited by this paper
• A new approach to protein fold recognition

  1992cited by this paper
• Neural network lipreading system for improved speech recognition

  1992cited by this paper
• Information processing in dynamical systems: foundations of harmony theory

  1986cited by this paper
• Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins.

  1974cited by this paper

• The integration of artificial intelligence and protein science: the protein structure prediction and protein design revolution behind the 2024 Nobel Prize in chemistry

  2025cites this paper
• AF2Ring: A Memory Efficient Method for Predicting Quaternary Structure of Cyclic Protein Oligomers

  2025cites this paper
• New insights into translational research in Alzheimer's disease guided by artificial intelligence, computational and systems biology

  2025cites this paper
• Artificial intelligence in orthopedics: fundamentals, current applications, and future perspectives

  2025cites this paper
• A Review on Intervention of AI in Pharmaceutical Sector: Revolutionizing Drug Discovery and Manufacturing

  2025cites this paper
• "The Impact of AI on Pharma R&D: Accelerating Innovation in Drug Developments"

  2025cites this paper
• IMPLEMENTING ARTIFICIAL INTELLIGENCE IN DRUG RESEARCH DEVELOPMENT

  2025cites this paper
• Industrial Automation using Artificial Intelligence

  2025cites this paper
• The Role of AI in Drug Discovery

  2024cites this paper
• The Rise of Artificial Intelligence in Pharma: Shaping the Future of Drug Discovery

  2024cites this paper
• A Survey on Computational Methods in Drug Discovery for Neurodegenerative Diseases

  2024cites this paper
• ProXplore: A GPU-Enhanced Protein Discovery Engine

  2024cites this paper
• A novel approach for protein secondary structure prediction using encoder–decoder with attention mechanism model

  2024cites this paper
• Deep learning in structural bioinformatics: current applications and future perspectives

  2024cites this paper
• MHTAPred-SS: A Highly Targeted Autoencoder-Driven Deep Multi-Task Learning Framework for Accurate Protein Secondary Structure Prediction

  2024cites this paper
• TEST-Net: transformer-enhanced Spatio-temporal network for infectious disease prediction

  2024cites this paper
• Studying protein-protein interactions: Latest and most popular approaches.

  2024cites this paper
• Deciphering Smells from SMILES Notation of the Chemical Compounds: A Deep Learning Approach

  2024cites this paper
• CNN-BLSTM based deep learning framework for eukaryotic kinome classification: An explainability based approach

  2024cites this paper
• The Application Mode of Multi-Dimensional Time Series Data Based on a Multi-Stage Neural Network

  2023cites this paper
• Effective Local and Secondary Protein Structure Prediction by Combining a Neural Network-Based Approach with Extensive Feature Design and Selection without Reliance on Evolutionary Information

  2023cites this paper
• Generating Adversarial Examples with Task Oriented Multi-Objective Optimization

  2023cites this paper
• Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms

  2023cites this paper
• DeepADRA2A: predicting adrenergic α2a inhibitors using deep learning

  2023cites this paper
• Rise of Deep Learning Clinical Applications and Challenges in Omics Data: A Systematic Review

  2023cites this paper
• Generating new protein sequences by using dense network and attention mechanism.

  2023cites this paper
• DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function

  2023influential citation
• A comprehensive framework for advanced protein classification and function prediction using synergistic approaches: Integrating bispectral analysis, machine learning, and deep learning

  2023cites this paper
• Prediction of Protein Secondary Structure based on Multi-scale Convolutional Neural Network

  2023cites this paper
• Real-time crash risk prediction in freeway tunnels considering features interaction and unobserved heterogeneity: A two-stage deep learning modeling framework

  2023cites this paper
• Visual feature-based improved EfficientNet-GRU for Fritillariae Cirrhosae Bulbus identification

  2023cites this paper
• Revisiting DeepFool: generalization and improvement

  2023cites this paper
• Deep Learning for Genomics: From Early Neural Nets to Modern Large Language Models

  2023cites this paper
• A Deep Learning Approach for Prediction of Protein Secondary Structure

  2022cites this paper
• In situ health monitoring of multiscale structures and its instantaneous verification using mechanoluminescence and dual machine learning

  2022cites this paper
• Empirical Study of Protein Feature Representation on Deep Belief Networks Trained With Small Data for Secondary Structure Prediction

  2022influential citation
• Protein Language Models and Structure Prediction: Connection and Progression

  2022cites this paper
• Energy Profile Bayes and Thompson Optimized Convolutional Neural Network protein structure prediction

  2022cites this paper
• Collectively encoding protein properties enriches protein language models

  2022cites this paper
• DL 101: Basic introduction to deep learning with its application in biomedical related fields

  2022cites this paper
• Deep Ensemble Learning with Atrous Spatial Pyramid Networks for Protein Secondary Structure Prediction

  2022cites this paper
• Enhancing the prediction of protein coding regions in biological sequence via a deep learning framework with hybrid encoding

  2022cites this paper
• Res-Dom: predicting protein domain boundary from sequence using deep residual network and Bi-LSTM

  2022cites this paper
• Different methods, techniques and their limitations in protein structure prediction: A review.

  2022cites this paper
• Protein–protein interaction prediction with deep learning: A comprehensive review

  2022cites this paper
• On Global-view Based Defense via Adversarial Attack and Defense Risk Guaranteed Bounds

  2022cites this paper
• A Progress on Protein Structure Prediction using Various Soft Computing Techniques

  2022cites this paper
• OneHotEncoding and LSTM-based deep learning models for protein secondary structure prediction

  2022cites this paper
• A Survey on Deep Networks Approaches in Prediction of Sequence-Based Protein–Protein Interactions

  2022cites this paper
• Multi-Level Analysis of Intrinsically Disordered Protein Docking Methods.

  2022cites this paper
• Improving protein secondary structure prediction by deep language models and transformer networks

  2022cites this paper
• Health Informatics: Engaging Modern Healthcare Units: A Brief Overview

  2022cites this paper
• PrMFTP: Multi-functional therapeutic peptides prediction based on multi-head self-attention mechanism and class weight optimization

  2022cites this paper
• Implementing Deep Learning Algorithm on Physicochemical Properties of Proteins

  2021cites this paper
• Predicting protein secondary structure based on ensemble Neural Network

  2021cites this paper
• Cascading 1D-Convnet Bidirectional Long Short Term Memory Network with Modified COCOB Optimizer: A Novel Approach for Protein Secondary Structure Prediction

  2021cites this paper
• Prediction of protein‐protein interactions using stacked auto‐encoder

  2021cites this paper
• Deep Learning-Based Drug Screening for COVID-19 and Case Studies

  2021cites this paper
• A deep neural network–based approach for prediction of mutagenicity of compounds

  2021cites this paper
• Deep Learning Classification of Systemic Sclerosis Skin Using the MobileNetV2 Model

  2021cites this paper
• Scada system for chemical water treatment plant of the thermoelectric power plant “José Martí”

  2021cites this paper
• Artificial Intelligence: A New Era in Drug Discovery

  2021cites this paper
• COVID-19 PATIENTS ANALYSIS AND RISK PREDICTION BASED ON LIFESTYLE DISEASES THROUGH INDIAN DATASET

  2021cites this paper
• Identification of Enzymes-specific Protein Domain Based on DDE, and Convolutional Neural Network

  2021cites this paper
• SMILES to Smell: Decoding the Structure-Odor Relationship of Chemical Compounds Using the Deep Neural Network Approach

  2021cites this paper
• Protein secondary structure prediction using a lightweight convolutional network and label distribution aware margin loss

  2021cites this paper
• Potential Applications of Deep Learning in Bioinformatics Big Data Analysis

  2021cites this paper
• An effective feature extraction with deep neural network architecture for protein-secondary-structure prediction

  2021cites this paper
• Integrated computation of corrosion: Modelling, simulation and applications

  2021cites this paper
• AI applications in functional genomics

  2021cites this paper
• GHS-NET a generic hybridized shallow neural network for multi-label biomedical text classification

  2021cites this paper
• An Integrated Deep Network for Cancer Survival Prediction Using Omics Data

  2021cites this paper
• Overview of Machine Learning Methods for Genome-Wide Association Analysis

  2021cites this paper
• Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery

  2021cites this paper
• Computational Methods and Tools in Antimicrobial Peptide Research

  2021cites this paper
• Explainable deep neural networks for novel viral genome prediction

  2021cites this paper
• Applications of artificial intelligence to drug design and discovery in the big data era: a comprehensive review

  2021cites this paper
• Machine Learning in Drug Discovery: A Review

  2021cites this paper
• Current directions in combining simulation-based macromolecular modeling approaches with deep learning

  2021cites this paper
• Computational intelligence techniques for automatic detection of Wi-Fi attacks in wireless IoT networks

  2021cites this paper
• Prediction of FMN Binding Sites in Electron Transport Chains Based on 2-D CNN and PSSM Profiles

  2021cites this paper
• Biological computation and computational biology: survey, challenges, and discussion

  2021cites this paper
• Convolutional neural network in proteomics and metabolomics for determination of comorbidity between cancer and schizophrenia

  2021cites this paper
• Deep Large-Scale Multitask Learning Network for Gene Expression Inference

  2020cites this paper
• Generating functional protein variants with variational autoencoders

  2020cites this paper
• [Progress in biomedical data analysis based on deep learning].

  2020cites this paper
• Set of Approaches Based on Position Specific Scoring Matrix and Amino Acid Sequence for Primary Category Enzyme Classification

  2020cites this paper
• Redundancy-weighting the PDB for detailed secondary structure prediction using deep-learning models

  2020cites this paper
• DeepAVP: A Dual-Channel Deep Neural Network for Identifying Variable-Length Antiviral Peptides

  2020cites this paper
• Deep Learning Theoretical Chapter for Chemometrician

  2020cites this paper
• Using Deep Neural Networks to Improve the Performance of Protein-Protein Interactions Prediction

  2020cites this paper
• Towards Robust DNNs: An Taylor Expansion-Based Method for Generating Powerful Adversarial Examples

  2020cites this paper
• Oil Spill Mapping from Kompsat-2 High-Resolution Image Using Directional Median Filtering and Artificial Neural Network

  2020cites this paper
• TEAM: An Taylor Expansion-Based Method for Generating Adversarial Examples

  2020cites this paper
• Clinical Applications of Antimicrobial Peptides (AMPs): where do we stand now?

  2020cites this paper
• A deep learning framework with hybrid encoding for protein coding regions prediction in biological sequences

  2020cites this paper
• iDHS-DASTS: identifying DNase I hypersensitive sites based on LASSO and stacking learning.

  2020cites this paper
• TargetDBP: Accurate DNA-Binding Protein Prediction Via Sequence-Based Multi-View Feature Learning

  2020cites this paper
• Bioimage-Based Prediction of Protein Subcellular Location in Human Tissue with Ensemble Features and Deep Networks

  2020cites this paper
• Risk evaluation of urban rainwater system waterlogging based on neural network and dynamic hydraulic model

  2020cites this paper