De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods

On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation

(2014) Wing-Cheong Wong et al.   BMC BIOINFORMATICS

Hybrid and Rogue Kinases Encoded in the Genomes of Model Eukaryotes

(2014) Ramaswamy Rakshambikai et al.   PLoS One

ECOD: An Evolutionary Classification of Protein Domains

(2014) Hua Cheng et al.   PLoS Computational Biology

Filling-in Void and Sparse Regions in Protein Sequence Space by Protein-Like Artificial Sequences Enables Remarkable Enhancement in Remote Homology Detection Capability

(2013) Richa Mudgal et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Ecogenomic Perspectives on Domains of Unknown Function: Correlation-Based Exploration of Marine Metagenomes

(2013) Pier Luigi Buttigieg et al.   PLoS One

MESSA: MEta-Server for protein Sequence Analysis

(2012) Qian Cong et al.   BMC BIOLOGY

dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

(2012) Hai Fang et al.   NUCLEIC ACIDS RESEARCH

A DECADE AFTER THE FIRST FULL HUMAN GENOME SEQUENCING: WHEN WILL WE UNDERSTAND OUR OWN GENOME?

(2012) FRANK EISENHABER   Journal of Bioinformatics and Computational Biology

Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins

(2011) Wing-Cheong Wong et al.   Biology Direct

AlignHUSH: Alignment of HMMs using structure and hydrophobicity information

(2011) Oruganty Krishnadev et al.   BMC BIOINFORMATICS

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

DUFs: families in search of function

(2010) Alex Bateman et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution

(2010) Marina V Omelchenko et al.   Biology Direct

The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam

(2010) Nalin C.W. Goonesekere et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination

(2009) Anna Lobley et al.   BIOINFORMATICS

The sequence–structure relationship and protein function prediction

(2009) M I Sadowski et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The origin of the electrostatic perturbation in acetoacetate decarboxylase

(2009) Meng-Chiao Ho et al.   NATURE

PROCAIN: protein profile comparison with assisting information

(2009) Yong Wang et al.   NUCLEIC ACIDS RESEARCH

Exploration of Uncharted Regions of the Protein Universe

(2009) Lukasz Jaroszewski et al.   PLOS BIOLOGY

An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations

(2009) Holly J. Atkinson et al.   PLoS Computational Biology

Profile Comparer: a program for scoring and aligning profile hidden Markov models

(2008) M. Madera   BIOINFORMATICS

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

(2008) David M Kristensen et al.   BMC BIOINFORMATICS

PROMALS3D: a tool for multiple protein sequence and structure alignments

(2008) Jimin Pei et al.   NUCLEIC ACIDS RESEARCH

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function

(2008) Marco Punta et al.   PLoS Computational Biology

Profile-profile comparisons by COMPASS predict intricate homologies between protein families

(2003) Ruslan I. Sadreyev et al.   PROTEIN SCIENCE