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

Bayesian nonparametrics in protein remote homology search

(2016) Mindaugas Margelevičius   BIOINFORMATICS

Protein Remote Homology Detection by Combining Pseudo Dimer Composition with an Ensemble Learning Method

(2016) Bin Liu et al.   Current Proteomics

Identification of DNA-Binding Proteins by Combining Auto-Cross Covariance Transformation and Ensemble Learning

(2016) Bin Liu et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Application of learning to rank to protein remote homology detection

(2015) Bin Liu et al.   BIOINFORMATICS

Exploratory Predicting Protein Folding Model with Random Forest and Hybrid Features

(2015) Xuewei Zhao et al.   Current Proteomics

IChemPIC: A Random Forest Classifier of Biological and Crystallographic Protein–Protein Interfaces

(2015) Franck Da Silva et al.   Journal of Chemical Information and Modeling

Protein remote homology detection by combining Chou’s distance-pair pseudo amino acid composition and principal component analysis

(2015) Bin Liu et al.   MOLECULAR GENETICS AND GENOMICS

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

(2015) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The value of protein structure classification information-Surveying the scientific literature

(2015) Naomi K. Fox et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects

(2014) Bin Liu et al.   BIOINFORMATICS

nDNA-prot: identification of DNA-binding proteins based on unbalanced classification

(2014) Li Song et al.   BMC BIOINFORMATICS

Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts

(2014) Qian Liu et al.   BMC BIOINFORMATICS

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

(2014) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

iDNA-Prot|dis: Identifying DNA-Binding Proteins by Incorporating Amino Acid Distance-Pairs and Reduced Alphabet Profile into the General Pseudo Amino Acid Composition

(2014) Bin Liu et al.   PLoS One

Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection

(2013) Bin Liu et al.   BIOINFORMATICS

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

(2013) Yang Shen et al.   JOURNAL OF BIOMOLECULAR NMR

Protein Remote Homology Detection by Combining Chou’s Pseudo Amino Acid Composition and Profile-Based Protein Representation

(2013) Bin Liu et al.   Molecular Informatics

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

(2013) Naomi K. Fox et al.   NUCLEIC ACIDS RESEARCH

The prediction of protein structural class using averaged chemical shifts

(2012) Hao Lin et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles

(2012) D. Gront et al.   NUCLEIC ACIDS RESEARCH

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

(2012) Shuji Suzuki et al.   PLoS One

A Global Characterization and Identification of Multifunctional Enzymes

(2012) Xian-Ying Cheng et al.   PLoS One

Using Amino Acid Physicochemical Distance Transformation for Fast Protein Remote Homology Detection

(2012) Bin Liu et al.   PLoS One

An assessment of substitution scores for protein profile–profile comparison

(2011) Xugang Ye et al.   BIOINFORMATICS

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

(2011) Y. Yang et al.   BIOINFORMATICS

Protein remote homology detection based on auto-cross covariance transformation

(2011) Xuan Liu et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Prediction of ketoacyl synthase family using reduced amino acid alphabets

(2011) Wei Chen et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

FFAS server: novel features and applications

(2011) L. Jaroszewski et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding

(2011) Iain Melvin et al.   PLoS Computational Biology

COMA server for protein distant homology search

(2010) Mindaugas Margelevičius et al.   BIOINFORMATICS

GPU-BLAST: using graphics processors to accelerate protein sequence alignment

(2010) P. D. Vouzis et al.   BIOINFORMATICS

Physicochemical property distributions for accurate and rapid pairwise protein homology detection

(2010) Bobbie-Jo M Webb-Robertson et al.   BMC BIOINFORMATICS

Prediction of thermophilic proteins using feature selection technique

(2010) Hao Lin et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Ongoing and future developments at the Universal Protein Resource

(2010)   NUCLEIC ACIDS RESEARCH

PROCAIN server for remote protein sequence similarity search

(2009) Y. Wang et al.   BIOINFORMATICS

Hidden Markov Models and their Applications in Biological Sequence Analysis

(2009) Byung-Jun Yoon   CURRENT GENOMICS

Semi-Supervised Learning (Chapelle, O. et al., Eds.; 2006) [Book reviews]

(2009) O. Chapelle et al.   IEEE TRANSACTIONS ON NEURAL NETWORKS

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

COMPASS server for homology detection: improved statistical accuracy, speed and functionality

(2009) R. I. Sadreyev et al.   NUCLEIC ACIDS RESEARCH

webPRC: the Profile Comparer for alignment-based searching of public domain databases

(2009) B. W. Brandt et al.   NUCLEIC ACIDS RESEARCH

PROSITE, a protein domain database for functional characterization and annotation

(2009) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

RANKPROP: a web server for protein remote homology detection

(2008) I. Melvin et al.   BIOINFORMATICS

SVM-HUSTLE--an iterative semi-supervised machine learning approach for pairwise protein remote homology detection

(2008) A. R. Shah et al.   BIOINFORMATICS

Probabilistic multi-class multi-kernel learning: on protein fold recognition and remote homology detection

(2008) Theodoros Damoulas et al.   BIOINFORMATICS

Word correlation matrices for protein sequence analysis and remote homology detection

(2008) Thomas Lingner et al.   BMC BIOINFORMATICS

Combining classifiers for improved classification of proteins from sequence or structure

(2008) Iain Melvin et al.   BMC BIOINFORMATICS

A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis

(2008) Bin Liu et al.   BMC BIOINFORMATICS

Protein structure databases with new web services for structural biology and biomedical research

(2008) D. M. Standley et al.   BRIEFINGS IN BIOINFORMATICS

A Constructive Hybrid Structure Optimization Methodology for Radial Basis Probabilistic Neural Networks

(2008) De-Shuang Huang et al.   IEEE TRANSACTIONS ON NEURAL NETWORKS

Remote protein homology detection using recurrence quantification analysis and amino acid physicochemical properties

(2008) Yuchen Yang et al.   JOURNAL OF THEORETICAL BIOLOGY