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The HSSP database of protein structure-sequence alignments

R Schneider
1996 Nucleic Acids Research  
For each protein of known 3-D structure from the Protein Data Bank (PDB), the database has a multiple sequence alignment of all available homologues and a sequence profile characteristic of the family.  ...  HSSP is a derived database merging structural (3-D) and sequence (1-D) information.  ...  INTRODUCTION HSSP (homology-derived structures of proteins) is a derived database merging information from 3-D structures and 1-D sequences of proteins.  ... 
doi:10.1093/nar/24.1.201 pmid:8594579 pmcid:PMC145595 fatcat:3ccy7ljdxneahjvboj7hpnpgwa

The HSSP database of protein structure-sequence alignments

R. Schneider, A. de Daruvar, C. Sander
1997 Nucleic Acids Research  
For each protein of known 3-D structure from the Protein Data Bank (PDB), the database has a multiple sequence alignment of all available homologues and a sequence profile characteristic of the family.  ...  HSSP is a derived database merging structural (3-D) and sequence (1-D) information.  ...  INTRODUCTION HSSP (homology-derived structures of proteins) is a derived database merging information from 3-D structures and 1-D sequences of proteins.  ... 
doi:10.1093/nar/25.1.226 pmid:9016541 pmcid:PMC146419 fatcat:mvbukkskcrd6fccipy23qmxd44

The HSSP database of protein structure-sequence alignments

C Sander, R Schneider
1994 Nucleic Acids Research  
For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.  ...  HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D).  ...  As a result, HSSP is not only a database of aligned sequence families, but also a database of implied secondary and tertiary structures.  ... 
pmid:7937066 pmcid:PMC308328 fatcat:t4bhso55mfalffup6vziag66ce

The HSSP database of protein structure-sequence alignments and family profiles

C Dodge
1998 Nucleic Acids Research  
For each protein of known 3D structure from the Protein Data Bank (PDB), we provide a multiple sequence alignment of putative homologues and a sequence profile characteristic of the protein family, centered  ...  HSSP (http://www.sander.embl-ebi.ac.uk/hssp/ ) is a derived database merging structure (3-D) and sequence (1-D) information.  ...  As a result, HSSP is not only a database of aligned sequence families, but also a database of implied secondary and tertiary structures.  ... 
doi:10.1093/nar/26.1.313 pmid:9399862 pmcid:PMC147243 fatcat:scaizqtbondlppxj3ralbjkydy

Protein folds and families: sequence and structure alignments

L. Holm, C. Sander
1999 Nucleic Acids Research  
As a result, the HSSP database not only provides aligned sequence families, but also implies secondary and tertiary structures covering 36% of all sequences in Swiss-Prot.  ...  In particular, this results in a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity.  ...  To exploit this principle, the HSSP database is generated by aligning, for each protein of known 3D structure in the PDB (1), all its likely sequence homologues.  ... 
doi:10.1093/nar/27.1.244 pmid:9847191 pmcid:PMC148146 fatcat:idrmaz6uebbb7imcsozkn3csza

The HSSP data base of protein structure — sequence alignments

Chris Sander, Reinhard Schneider
1993 Nucleic Acids Research  
Tertiary structure models can be built by fitting the sequence of the homologue, as aligned, into the 3-D template of the protein of known structure.  ...  The database is useful for the analysis of residue conservation in structural context, for the definition of structurally meaningful sequence patterns, and for other questions of protein evolution, folding  ...  (22.0) total number of alignments in the HSSP database 37715 43266 45140 49784 number of unique alignments and fraction of SWISS-PROT in the HSSP database* 3065 (15.3%) 3498 (15.4%)  ... 
doi:10.1093/nar/21.13.3105 pmid:8332531 pmcid:PMC309738 fatcat:m5z5xhweo5edfn4ywokd4jro6y

The PSSH database of alignments between protein sequences and tertiary structures

A. Schafferhans
2003 Nucleic Acids Research  
We introduce the PSSH ('Protein Sequence-to-Structure Homologies') database derived from HSSP2, an improved version of the HSSP ('Homology-derived Secondary Structure of Proteins') database [Dodge et al  ...  Whereas each HSSP entry lists all protein sequences related to a given 3D structure, PSSH is the 'inverse', with each entry listing all structures related to a given sequence.  ...  This work was partly funded by a grant from the German Federal Ministry for Science and Education ('Protein Structure Factory' grant 01 GG 9817).  ... 
doi:10.1093/nar/gkg110 pmid:12520061 pmcid:PMC165557 fatcat:4tb6jl65m5duvh3wfyykefhwwi

Building multiple sequence alignments with a flavor of HSSP alignments

Roberto Hiroshi Higa, Sergio Aparecido Braga da Cruz, Paula Regina Kuser, Michel Eduardo Beleza Yamagishi, Renato Fileto, Stanley Robson de Medeiros Oliveira, Ivan Mazoni, Edgard Henrique dos Santos, Adauto Luiz Mancini, Goran Neshich
2006 Genetics and Molecular Research  
Homology-derived secondary structure of proteins (HSSP) is a well-known database of multiple sequence alignments (MSAs) which merges information of protein sequences and their three-dimensional structures  ...  The present study describes a new method and its corresponding databank (SH2QS--database of sequences homologue to the query [structure-having] sequence).  ...  Jorge Hernandez Fernandez for providing data about conservation for the modeled structure of ACEn.  ... 
pmid:16755504 fatcat:nojyimwpb5asjabcyz3gyjxckm

ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure

R. H. Higa, A. J. Montagner, R. C. Togawa, P. R. Kuser, M. E. B. Yamagishi, A. L. Mancini, G. Pappas, R. T. Miura, L. G. Horita, G. Neshich
2004 Bioinformatics  
ConSSeq graphically represents information about amino acid conservation based on sequence alignments reported in homology-derived structures of proteins.  ...  Beyond the relative entropy for each position in the alignment, ConSSeq also presents the consensus sequence and information about the amino acids, which are predominant at each position of the alignment  ...  Homology-derived structures of proteins is a derived database merging information on three-dimensional (3D) protein structures and sequences of homologous proteins.  ... 
doi:10.1093/bioinformatics/bth185 pmid:15044236 fatcat:d2exytv5xngnlnecrmztwofabu

Sequence conserved for subcellular localization

Rajesh Nair, Burkhard Rost
2009 Protein Science  
The more proteins diverged in sequence, the more difficult it becomes for bioinformatics to infer similarities of protein function and structure from sequence.  ...  We found that a simple measure for sequence similarity accounting for pairwise sequence identity and alignment length, the HSSP distance, distinguished accurately between protein pairs of identical and  ...  The work of R.N. and B.R. was supported by the grants 1-P50-GM62413-01 and RO1-GM63029-01 from the National Institute of Health.  ... 
doi:10.1110/ps.0207402 pmid:12441382 pmcid:PMC2373743 fatcat:ytnf5zprybch5ll5v2nzzc2vwy

The ConSurf-HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures

Fabian Glaser, Yossi Rosenberg, Amit Kessel, Tal Pupko, Nir Ben-Tal
2004 Proteins: Structure, Function, and Bioinformatics  
The HSSP (Homology-Derived Secondary Structure of Proteins) database provides multiple sequence alignments (MSAs) for proteins of known three-dimensional (3D) structure in the Protein Data Bank (PDB).  ...  ) are occasionally important to maintain the 3D structure and biological function(s) of the protein.  ...  We are grateful to the Bioinformatics Service Unit of the George S. Wise Faculty of Life Sciences at Tel Aviv University for providing technical assistance and computational facilities.  ... 
doi:10.1002/prot.20305 pmid:15614759 fatcat:zohflozlq5ebbi7x3z3isv6qui

Twilight zone of protein sequence alignments

Burkhard Rost
1999 Protein Engineering Design & Selection  
Sequence alignments unambiguously distinguish between protein pairs of similar and non-similar structure when the pairwise sequence identity is high (>40% for long alignments).  ...  All findings are applicable to automatic database searches. Keywords: alignment quality analysis/evolutionary conservation/ genome analysis/protein sequence alignment/sequence space hopping  ...  Last, but not least, thanks to all those who deposit experimental information about protein structures and sequences in public databases, and to those maintaining these sources of knowledge.  ... 
doi:10.1093/protein/12.2.85 pmid:10195279 fatcat:7jwtlbkhkngx7p5cusr74odyyu

UniqueProt: creating representative protein sequence sets

S. Mika
2003 Nucleic Acids Research  
UniqueProt is a practical and easy to use web service designed to create representative, unbiased data sets of protein sequences.  ...  The largest possible representative sets are found through a simple greedy algorithm using the HSSP-value to establish sequence similarity.  ...  This work was supported by the grants RO1-GM63029-01 from the National Institute of Health (NIH) and 1-R01-LM07329-01 from the National Library of Medicine (NLM).  ... 
doi:10.1093/nar/gkg620 pmid:12824419 pmcid:PMC169026 fatcat:kkymoqvkardlno3ouazutqpxre

A series of PDB related databases for everyday needs

R. P. Joosten, T. A. H. te Beek, E. Krieger, M. L. Hekkelman, R. W. W. Hooft, R. Schneider, C. Sander, G. Vriend
2010 Nucleic Acids Research  
HSSP holds a multiple sequence alignment for all proteins. The PDBFINDER holds easy to parse summaries of the PDB file content, augmented with essentials from the other systems.  ...  The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series of databases that run parallel to the PDB.  ...  ACKNOWLEDGEMENTS The authors are especially grateful to those users of these databases who cite the related articles and who report problems.  ... 
doi:10.1093/nar/gkq1105 pmid:21071423 pmcid:PMC3013697 fatcat:jl2ocrg3v5avbgz7cdxbs3rsie

Discovering empirically conserved amino acid substitution groups in databases of protein families

T D Wu, D L Brutlag
1996 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
The matrix tabulates information from a database of protein families that contains numerous aligned positions.  ...  The algorithm is applied to the BLOCKS and HSSP databases. Twenty amino acid substitution groups are found to be conserved empirically in both databases.  ...  Acknowledgments This work was supported in part by grants LM 05716 and LM 07033 from the National Library of Medicine. The authors thank Tod Klingler for valuable discussions.  ... 
pmid:8877523 fatcat:byjvsylvejd4daahzdqbyeo7p4
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