Predicting protein function from sequence and structure
While the number of sequenced genomes continues to grow, experimentally verified
functional annotation of whole genomes remains patchy. Structural genomics projects are …
functional annotation of whole genomes remains patchy. Structural genomics projects are …
Advances and pitfalls of protein structural alignment
H Hasegawa, L Holm - Current opinion in structural biology, 2009 - Elsevier
Structure comparison opens a window into the distant past of protein evolution, which has
been unreachable by sequence comparison alone. With 55000 entries in the Protein Data …
been unreachable by sequence comparison alone. With 55000 entries in the Protein Data …
DALI and the persistence of protein shape
L Holm - Protein Science, 2020 - Wiley Online Library
DALI is a popular resource for comparing protein structures. The software is based on
distance‐matrix alignment. The associated web server provides tools to navigate, integrate …
distance‐matrix alignment. The associated web server provides tools to navigate, integrate …
CATH: an expanded resource to predict protein function through structure and sequence
The latest version of the CATH-Gene3D protein structure classification database has
recently been released (version 4.1, http://www. cathdb. info). The resource comprises over …
recently been released (version 4.1, http://www. cathdb. info). The resource comprises over …
FATCAT 2.0: towards a better understanding of the structural diversity of proteins
Abstract FATCAT 2.0 server (http://fatcat. godziklab. org/), provides access to a flexible
protein structure alignment algorithm developed in our group. In such an alignment …
protein structure alignment algorithm developed in our group. In such an alignment …
TM-align: a protein structure alignment algorithm based on the TM-score
Y Zhang, J Skolnick - Nucleic acids research, 2005 - academic.oup.com
We have developed TM-align, a new algorithm to identify the best structural alignment
between protein pairs that combines the TM-score rotation matrix and Dynamic …
between protein pairs that combines the TM-score rotation matrix and Dynamic …
How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis
M Vihinen - BMC genomics, 2012 - Springer
Background Prediction methods are increasingly used in biosciences to forecast diverse
features and characteristics. Binary two-state classifiers are the most common applications …
features and characteristics. Binary two-state classifiers are the most common applications …
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee
Expresso is a multiple sequence alignment server that aligns sequences using structural
information. The user only needs to provide sequences. The server runs BLAST to identify …
information. The user only needs to provide sequences. The server runs BLAST to identify …
Upcoming challenges for multiple sequence alignment methods in the high-throughput era
C Kemena, C Notredame - Bioinformatics, 2009 - academic.oup.com
This review focuses on recent trends in multiple sequence alignment tools. It describes the
latest algorithmic improvements including the extension of consistency-based methods to …
latest algorithmic improvements including the extension of consistency-based methods to …
[HTML][HTML] Enhanced fold recognition using efficient short fragment clustering
E Krissinel - Journal of molecular biochemistry, 2012 - ncbi.nlm.nih.gov
The main structure aligner in the CCP4 Software Suite, SSM (Secondary Structure Matching)
has a limited applicability on the intermediate stages of the structure solution process, when …
has a limited applicability on the intermediate stages of the structure solution process, when …