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FlexSnap: Flexible Non-sequential Protein Structure Alignment [chapter]

Saeed Salem, Mohammed J. Zaki, Chris Bystroff
2009 Lecture Notes in Computer Science  
We propose the FlexSnap algorithm for flexible nontopological protein structural alignment.  ...  Results: The effectiveness of FlexSnap is demonstrated by measuring the agreement of its alignments with manually curated non-sequential structural alignments.  ...  Also, we thank the authors of the different alignment algorithms for making their programs available.  ... 
doi:10.1007/978-3-642-04241-6_23 fatcat:o5qmps3imnfvnlj7fhkm3pkl5a

FlexSnap: Flexible Non-sequential Protein Structure Alignment

Saeed Salem, Mohammed J Zaki, Chris Bystroff
2010 Algorithms for Molecular Biology  
We propose the FlexSnap algorithm for flexible non-topological protein structural alignment.  ...  The effectiveness of FlexSnap is demonstrated by measuring the agreement of its alignments with manually curated non-sequential structural alignments.  ...  permutation of the bold letters in Flexible non-Sequential protein Alignment  ... 
doi:10.1186/1748-7188-5-12 pmid:20047669 pmcid:PMC2846951 fatcat:tekslm35vvdn7jx6yly6333a2u

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic

Peter Brown, Wayne Pullan, Yuedong Yang, Yaoqi Zhou
2015 Bioinformatics  
This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique.  ...  alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments.  ...  Fig. 4 . 4 Structure alignments of protein pair 2ES9-1SXJ, includes non-sequential alignment from SPalignNS (left), sequential alignment from SPalign (middle) and non-sequential alignment from CLICK (right  ... 
doi:10.1093/bioinformatics/btv580 pmid:26454279 fatcat:itcebabpkbgavlevwiw2e67the

Flexible Protein Structure Alignment Based on Topology String Alignment of Secondary Structure

Jafar Razmara
2014 International Journal of e-Education, e-Business, e-Management and e-Learning  
Index Terms-Protein structure alignment, flexible alignment, structure comparison.  ...  The paper reports a method for flexible alignment of protein structure.  ...  Moreover, FlexSnap [14] is a greedy chaining algorithm for flexible sequential and non-sequential alignment of protein structure.  ... 
doi:10.7763/ijeeee.2014.v4.294 fatcat:3rexvmjocrh3naqr7ecg26asd4

A local average distance descriptor for flexible protein structure comparison

Hsin-Wei Wang, Chia-Han Chu, Wen-Ching Wang, Tun-Wen Pai
2014 BMC Bioinformatics  
Protein structures are flexible and often show conformational changes upon binding to other molecules to exert biological functions.  ...  Results: In this paper, we propose a novel descriptor, local average distance (LAD), based on either the geodesic distances (GDs) or Euclidean distances (EDs) for pairwise flexible protein structure comparison  ...  Both FlexProt and FATCAT are sequential alignment algorithms thus unable to identify non-sequential alignments.  ... 
doi:10.1186/1471-2105-15-95 pmid:24694083 pmcid:PMC3992163 fatcat:de2nss64jfhvzkyeb6vqxddmuq

Calculating and scoring high quality multiple flexible protein structure alignments

David W. Ritchie
2016 Bioinformatics  
Calculating and scoring high quality multiple flexible protein structure alignments.  ...  In contrast, both Matt and Kpax calculate strictly sequential MSAs which do not allow non-sequential permutations of residues.  ...  Because several of the SISY reference alignments contain non-sequential SAs that cannot be fully aligned by sequential aligners, these datasets are grouped separately in Table 3 (denoted as "seq" and  ... 
doi:10.1093/bioinformatics/btw300 pmid:27187202 fatcat:jpeeknjkrzfivevhztsg2nfrhu

Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection

Guillaume Chapuis, Mathilde Le Boudic-Jamin, Rumen Andonov, Hristo Djidjev, Dominique Lavenier
2015 Scientific Programming  
as well as to detect structural repetitions within a single protein.  ...  Finding similarities between protein structures is a crucial task in molecular biology.  ...  Such an approach allows to introduce flexibility and non-sequentiality in protein structure alignments.  ... 
doi:10.1155/2015/279715 fatcat:a5lizhbu4vfjdbugxefw2pnm5u

Protein structure and evolution

JE Sykes
2021
The first is a benchmarking study of protein structure alignment methods, with efficacy assessed through their ability to determine levels of structural similarity between protein domains and to cluster  ...  Sorting proteins by structure is relevant to many biochemical problems, including constructing networks based on structural similarity.  ...  There are also a number of methods that do this whilst adjusting, to varying extents, for flexibility of proteins [61; 62] and non-sequential alignments [25] .  ... 
doi:10.25959/100.00037906 fatcat:lubrdexyovdi5lvbum2ikpolrq