DALI and the persistence of protein shape

Non-sequential protein structure alignment by conformational space annealing and local refinement

(2019) InSuk Joung et al.   PLoS One

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Benchmarking fold detection by DaliLite v.5

(2019) Liisa Holm   BIOINFORMATICS

PANNZER2: a rapid functional annotation web server

(2018) Petri Törönen et al.   NUCLEIC ACIDS RESEARCH

SCOPe: classification of large macromolecular structures in the structural classification of proteins—extended database

(2018) John-Marc Chandonia et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Multiple origins of viral capsid proteins from cellular ancestors

(2017) Mart Krupovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

(2017) Stephen K. Burley et al.   PROTEIN SCIENCE

Dali server update

(2016) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

CATH: an expanded resource to predict protein function through structure and sequence

(2016) Natalie L. Dawson et al.   NUCLEIC ACIDS RESEARCH

UniAlign: protein structure alignment meets evolution

(2015) Chunyu Zhao et al.   BIOINFORMATICS

SANSparallel: interactive homology search against Uniprot

(2015) Panu Somervuo et al.   NUCLEIC ACIDS RESEARCH

Manual classification strategies in the ECOD database

(2015) Hua Cheng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models

(2014) Travis J Wheeler et al.   BMC BIOINFORMATICS

Protein structure alignment beyond spatial proximity

(2013) Sheng Wang et al.   Scientific Reports

Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments

(2012) A. W. Slater et al.   BIOINFORMATICS

DALIX: Optimal DALI Protein Structure Alignment

(2012) Inken Wohlers et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Exploring the limits of fold discrimination by structural alignment: A large scale benchmark using decoys of known fold

(2011) Siv Midtun Hollup et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Dali server: conservation mapping in 3D

(2010) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

Protein domain assignment from the recurrence of locally similar structures

(2010) Chin-Hsien Tai et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Advances and pitfalls of protein structural alignment

(2009) Hitomi Hasegawa et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space

(2009) Alison Cuff et al.   STRUCTURE

Protein structure alignment considering phenotypic plasticity

(2008) G. Csaba et al.   BIOINFORMATICS

Searching protein structure databases with DaliLite v.3

(2008) L. Holm et al.   BIOINFORMATICS