Protein structure alignment using elastic shape analysis
W Liu, A Srivastava, J Zhang - Proceedings of the First ACM International …, 2010 - dl.acm.org
In this paper we present a method for flexible protein structure alignment based on elastic
shape analysis of backbones, in a manner that can incorporate different characteristics of …
shape analysis of backbones, in a manner that can incorporate different characteristics of …
Development and validation of a consistency based multiple structure alignment algorithm
J Ebert, D Brutlag - Bioinformatics, 2006 - academic.oup.com
We introduce an algorithm that uses the information gained from simultaneous consideration
of an entire group of related proteins to create multiple structure alignments (MSTAs) …
of an entire group of related proteins to create multiple structure alignments (MSTAs) …
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures
V Alexandrov, M Gerstein - BMC bioinformatics, 2004 - Springer
Abstract Background Hidden Markov Models (HMMs) have proven very useful in
computational biology for such applications as sequence pattern matching, gene-finding …
computational biology for such applications as sequence pattern matching, gene-finding …
Calculating and scoring high quality multiple flexible protein structure alignments
DW Ritchie - Bioinformatics, 2016 - academic.oup.com
Motivation: Calculating multiple protein structure alignments (MSAs) is important for
understanding functional and evolutionary relationships between protein families, and for …
understanding functional and evolutionary relationships between protein families, and for …
[PDF][PDF] Regression analysis of multiple protein structures
TD Wu, T Hastie, SC Schmidler… - Proceedings of the second …, 1998 - dl.acm.org
A general framework is presented for analyzing multiple protein structures. A family of
related protein structures may be analyzed using statistical regression methods. The …
related protein structures may be analyzed using statistical regression methods. The …
Progressive combinatorial algorithm for multiple structural alignments: application to distantly related proteins
ME Ochagavia, S Wodak - Proteins: Structure, Function, and …, 2004 - Wiley Online Library
MALECON is a progressive combinatorial procedure for multiple alignments of protein
structures. It searches a library of pairwise alignments for all three‐protein alignments in …
structures. It searches a library of pairwise alignments for all three‐protein alignments in …
Recent progress in measuring structural similarity between proteins
O Carugo - Current protein and peptide science, 2007 - ingentaconnect.com
Surprisingly, after at least two decades of researches focused on the analysis of the
similarity between protein three-dimensional structures, several new comparison methods …
similarity between protein three-dimensional structures, several new comparison methods …
Improving model construction of profile HMMs for remote homology detection through structural alignment
Background Remote homology detection is a challenging problem in Bioinformatics.
Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful …
Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful …
From structure to function: methods and applications
HJ Wolfson, M Shatsky… - Current Protein and …, 2005 - ingentaconnect.com
The rapid increase in experimental data along with recent progress in computational
methods has brought modern biology a step closer toward solving one of the most …
methods has brought modern biology a step closer toward solving one of the most …
Comparative protein structure prediction
MA Marti‐Renom, B Yerkovich… - Current Protocols in …, 2002 - Wiley Online Library
Functional characterization of a protein sequence is one of the most frequent problems in
biology. In the absence of an experimentally determined structure, comparative or homology …
biology. In the absence of an experimentally determined structure, comparative or homology …