Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity

TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison

(2012) Jafar Razmara et al.   Algorithms for Molecular Biology

Detection of Spatial Correlations in Protein Structures and Molecular Complexes

(2012) Manfred J. Sippl et al.   STRUCTURE

GOSSIP: a method for fast and accurate global alignment of protein structures

(2011) I. Kifer et al.   BIOINFORMATICS

A Spectral Approach to Protein Structure Alignment

(2011) Y Shibberu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Maximum Contact Map Overlap Revisited

(2011) Rumen Andonov et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Representing and comparing protein folds and fold families using three-dimensional shape-density representations

(2011) Lazaros Mavridis et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

FlexSnap: Flexible Non-sequential Protein Structure Alignment

(2010) Saeed Salem et al.   Algorithms for Molecular Biology

Towards optimal alignment of protein structure distance matrices

(2010) Inken Wohlers et al.   BIOINFORMATICS

Pre-calculated protein structure alignments at the RCSB PDB website: Fig. 1.

(2010) Andreas Prlić et al.   BIOINFORMATICS

ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures

(2010) R. Sabarinathan et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

deconSTRUCT: general purpose protein database search on the substructure level

(2010) Zong Hong Zhang et al.   NUCLEIC ACIDS RESEARCH

FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately

(2010) Inbal Budowski-Tal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins

(2010) Mark Gerstein et al.   PROTEIN SCIENCE

Protein structure alignment based on internal coordinates

(2010) Yue-Feng Shen et al.   Interdisciplinary Sciences-Computational Life Sciences

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

(2009) Shashi Pandit et al.   BMC BIOINFORMATICS

Tableau-based protein substructure search using quadratic programming

(2009) Alex Stivala et al.   BMC BIOINFORMATICS

Advances and pitfalls of protein structural alignment

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

TRIAL: A Tool for Finding Distant Structural Similarities

(2009) Jayendra Venkateswaran et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Integrated search and alignment of protein structures

(2008) A. Sacan et al.   BIOINFORMATICS

A note on difficult structure alignment problems

(2008) M. J. Sippl et al.   BIOINFORMATICS

Structural search and retrieval using a tableau representation of protein folding patterns

(2008) Arun S. Konagurthu et al.   BIOINFORMATICS

Searching protein structure databases with DaliLite v.3

(2008) L. Holm et al.   BIOINFORMATICS

The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies

(2008) A. L. Cuff et al.   NUCLEIC ACIDS RESEARCH

MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison

(2002) Angel R. Ortiz et al.   PROTEIN SCIENCE