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PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe

Pritha Ghosh, Teerna Bhattacharyya, Oommen K Mathew, Ramanathan Sowdhamini
2019 Database: The Journal of Biological Databases and Curation  
Protein Alignments organized as Structural Superfamilies (PASS2) is a database that provides such alignments of members of protein domain superfamilies of known structure and with less than 40% sequence  ...  Structure-based sequence alignments of distantly related proteins enable the investigation of structural, evolutionary and functional relationships between proteins and their domains leading to their common  ...  Conflict of interest. None declared.  ... 
doi:10.1093/database/baz028 pmid:30820573 pmcid:PMC6395796 fatcat:oqj3l6eke5gqxljvsywuonnxjm

PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe

Teerna Bhattacharyya, Soumya Nayak, Smit Goswami, Vasundhara Gadiyaram, Oommen K Mathew, Ramanathan Sowdhamini
2022 Database: The Journal of Biological Databases and Curation  
Protein Alignment organized as Structural Superfamilies or PASS2 database provides such sequence alignments of protein domains within a superfamily as per the Structural Classification of Proteins extended  ...  Protein domains that are deviant from the rest of the members of a superfamily may compromise the quality of the alignment, and we found this to be the case in ∼7% of the total superfamilies we considered  ...  Protein Alignment organized as Structural Superfamilies (PASS2) is a database that provides structure-based sequence alignments of protein domains within a SCOPe superfamily 2 Database, Vol. 2022, Article  ... 
doi:10.1093/database/baac025 pmid:35411388 pmcid:PMC9216583 fatcat:fduzhi5jnvgcbmjzde6oy7ryai

PASS2: an automated database of protein alignments organised as structural superfamilies

Anirban Bhaduri, Ganesan Pugalenthi, Ramanathan Sowdhamini
2004 BMC Bioinformatics  
Organization of structure-based sequence alignments for distantly related proteins, provides a map of the conserved and critical regions of the protein universe that is useful for the analysis of folding  ...  The Protein Alignment organised as Structural Superfamily (PASS2) database represents continuously updated, structural alignments for evolutionary related, sequentially distant proteins.  ...  Acknowledgements R.S. is a Senior Research Fellow funded by the Wellcome Trust, U.K. GP is supported by the Wellcome Trust. Financial and infrastructural support from NCBS (TIFR) is also acknowledged.  ... 
doi:10.1186/1471-2105-5-35 pmid:15059245 pmcid:PMC407847 fatcat:dqikugesjbaqxkf7i6moo4jiy4

PASS2: a semi-automated database of Protein Alignments Organised as Structural Superfamilies

V. Mallika
2002 Nucleic Acids Research  
Sowdhamini is a recipient of Wellcome Trust Senior Research Fellowship and V. Mallika is supported by the Wellcome Trust.  ...  Selection of the Members for the Database. One representative protein domain entry, of the best resolution and R-factor from each family, is chosen for a preliminary alignment.  ...  The genome sequences, which are either homologues or additional superfamily members, are aligned with the original structure-based alignment and reannotated using JOY [9] .  ... 
doi:10.1093/nar/30.1.284 pmid:11752316 pmcid:PMC99156 fatcat:3vpmbjwhrnde3ou4m6qbjqkvrm

PASS2 version 4: An update to the database of structure-based sequence alignments of structural domain superfamilies

A. Gandhimathi, Anu G. Nair, R. Sowdhamini
2011 Nucleic Acids Research  
Accurate structure-based sequence alignments of distantly related proteins are crucial in gaining insight about protein domains that belong to a superfamily.  ...  The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.  ...  ACKNOWLEDGEMENTS A.G is supported by Senior Research Fellowship from the Council of Scientific and Industrial Research (CSIR) Government of India. We thank Dr Kanagarajadurai and Ms. S.  ... 
doi:10.1093/nar/gkr1096 pmid:22123743 pmcid:PMC3245109 fatcat:snsqznpzofc35lpjkrqio6xl4m

PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features

Arumugam Gandhimathi, Pritha Ghosh, Sridhar Hariharaputran, Oommen K. Mathew, R. Sowdhamini
2015 Nucleic Acids Research  
PASS2 is a database that records such alignments for protein domain superfamilies and has been constantly updated periodically.  ...  Structure-based sequence alignment is an essential step in assessing and analysing the relationship of distantly related proteins.  ...  CONCLUSION PASS2 database provides structure-based sequence alignments of protein domain superfamilies in correspondence with SCOP definitions.  ... 
doi:10.1093/nar/gkv1205 pmid:26553811 pmcid:PMC4702857 fatcat:hjm3irjarnd4riqkj45sd3mh2u

LenVarDB: database of length-variant protein domains

Eshita Mutt, Oommen K. Mathew, Ramanathan Sowdhamini
2013 Nucleic Acids Research  
Alignment of sequence homologues corresponding to a structural domain is available, starting from a structure-based sequence alignment of the superfamily.  ...  (PASS2) database, across 731 structural classification of proteins (SCOP)-based protein domain superfamilies connected to 2 730 625 sequence homologues.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt1014 pmid:24194591 pmcid:PMC3964994 fatcat:venfzsyngbbfpaunonzt22lnfy

Structural updates of alignment of protein domains and consequences on evolutionary models of domain superfamilies

Eshita Mutt, Sudha Sane Rani, Ramanathan Sowdhamini
2013 BioData Mining  
PASS2 is a database that retains structure-based sequence alignments of protein domain superfamilies and relies on SCOP database for its hierarchy and definition of superfamily members.  ...  Influx of newly determined crystal structures into primary structural databases is increasing at a rapid pace.  ...  The work is supported by Centre of Excellence Grant (BT/01/09) by Department of Biotechnology, India. EM, SS and RS wishes to thank NCBS (TIFR) for infrastructural and financial support.  ... 
doi:10.1186/1756-0381-6-20 pmid:24237883 pmcid:PMC4175504 fatcat:kpdipl7z3fcktmuhnai4sq6vay

GenDiS: Genomic Distribution of protein structural domain Superfamilies

G. Pugalenthi
2004 Nucleic Acids Research  
GenDiS database provides a survey of protein domains enlisted in sequence databases employing a 3-fold sequence search approach.  ...  The database on Genomic Distribution of protein structural domain Superfamilies (GenDiS) provides record for the distribution of 4001 protein domains organized as 1194 structural superfamilies across 18  ...  ACKNOWLEDGEMENTS R.S. is a Senior Research Fellow of the Wellcome Trust (UK). G.P. is also supported by the Wellcome Trust. We also thank NCBS (TIFR) for infrastructural support.  ... 
doi:10.1093/nar/gki087 pmid:15608190 pmcid:PMC540041 fatcat:phpvfvkktnfpjaczjldxvrpcfy

Improved performance of sequence search algorithms in remote homology detection

Adwait Govind Joshi, Upadhyayula Surya Raghavender, Ramanathan Sowdhamini
2013 F1000Research  
Bhaduri A, Pugalenthi G, Sowdhamini R: PASS2: an automated database of protein alignments organised as structural superfamilies. BMC Bioinformatics. 2004; 5: 35.  ...  Pugalenthi G, Bhaduri A, Sowdhamini R: GenDiS: Genomic Distribution of protein structural domain Superfamilies. Nucleic Acids Res. 2005; 33(Database issue): D252-D255.  ...  Acknowledgments All authors thank NCBS for infrastructural and general support. of the manuscript and both USR and RS contributed to the improvement of the manuscript.  ... 
doi:10.12688/f1000research.2-93.v1 pmid:25469226 pmcid:PMC4240247 fatcat:wp7yyoyz4retpkdjipi7z7ymuy

S4: structure-based sequence alignments of SCOP superfamilies

J. Casbon
2004 Nucleic Acids Research  
S4 is an automatically generated database of multiple structure-based sequence alignments of protein superfamilies in the SCOP database.  ...  All structural domains that do not share more than 40% sequence identity as defined by the ASTRAL compendium of protein structures are included.  ...  S4 (structure-based sequence alignments of SCOP superfamilies) provides multiple structure-based alignments of SCOP (version 1.63) protein superfamilies where no two domains share more than 40% sequence  ... 
doi:10.1093/nar/gki043 pmid:15608181 pmcid:PMC539997 fatcat:wluivkaxlnha7gif4nn3hiwawi

Improved performance of sequence search approaches in remote homology detection

Adwait Govind Joshi, Upadhyayula Surya Raghavender, Ramanathan Sowdhamini
2014 F1000Research  
This data mining approach has been applied to the entire structural superfamily database.  ...  We have used iterative profile-based methods, along with constraints of sequence motifs, to specify search directions.  ...  Having said that, some of the strategies, search directions and parameters depend on the sequence dispersion and population of families and few decisions are highly family-specific.  ... 
doi:10.12688/f1000research.2-93.v2 pmid:25469226 pmcid:PMC4240247 fatcat:maranugd4ng7rdujqbhkdg4dvy

Rebelling for a Reason: Protein Structural "Outliers"

Gandhimathi Arumugam, Anu G. Nair, Sridhar Hariharaputran, Sowdhamini Ramanathan, Jens Kleinjung
2013 PLoS ONE  
Structure-based sequence alignment of distantly related proteins, organized in PASS2 database, provides clues about structurally conserved regions among different functional families.  ...  This paper analyses the impact of structural divergence on function for multi-member superfamilies, selected from the PASS2 superfamily alignment database.  ...  Methods Structure-based Sequence Alignment of Superfamily Domains PASS2 [28] database contains structure-based sequence alignment of protein domain superfamilies in correspondence with SCOP 1.75.  ... 
doi:10.1371/journal.pone.0074416 pmid:24073209 pmcid:PMC3779223 fatcat:fcvoo7ky35gpxoofxee3fllfim

Regions of minimal structural variation among members of protein domain superfamilies: application to remote homology detection and modelling using distant relationships

Saikat Chakrabarti, R. Sowdhamini
2004 FEBS Letters  
packing and extent of structural deviations in 179 aligned members of superfamilies involving 1208 pairs of protein domains.  ...  , than fulllength alignments suggesting that they form the minimum structural requirement of a superfamily.  ...  Srinivasan for critical reading of the manuscript and for useful discussions. R.S. is a Senior Research Fellow funded by the Wellcome Trust Grant.  ... 
doi:10.1016/j.febslet.2004.05.028 pmid:15225604 fatcat:v3g7oy7jz5aqlefp4wcfnxfbpm

CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations

Sankaran Sandhya, Barah Pankaj, Madabosse Govind, Bernard Offmann, Narayanaswamy Srinivasan, Ramanathan Sowdhamini
2008 BMC Structural Biology  
On a non-redundant dataset of 353 domain superfamily alignments from PASS2, we find that 'length-deviant' protein superfamilies show > 30% length variation from their average domain length. 60% of additional  ...  Results: CUSP, examines protein domain structural alignments to distinguish regions of conserved structure common to related proteins from structurally unconserved regions that vary in length and type  ...  Acknowledgements R.S was an International Senior Research Fellow of the Wellcome Trust, U.K. S.S thanks the Council of Scientific and Industrial Research, India for PhD research fellowship.  ... 
doi:10.1186/1472-6807-8-28 pmid:18513436 pmcid:PMC2423364 fatcat:exzktzy7rnguxeyra5jm52fwxe
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