CDD: a database of conserved domain alignments with links to domain three-dimensional structure

Keywords

Conserved sequence, Biology, Sequence alignment, Computational biology, Domain (mathematical analysis)

References

• Profile analysis: detection of distantly related proteins.Michael Gribskov, A. McLachlan, David Eisenberg — 1987
• Embedding strategies for effective use of information from multiple sequence alignmentsSteven Henikoff, Jorja G. Henikoff — 1997
• Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods.Jong Moon Park, Kevin Karplus, Christian Barrett — 1998
• Cn3D: sequence and structure views for Entrez.Yanli Wang, Lewis Y. Geer, Colombe Chappey — 2000
• Database resources of the National Center for Biotechnology Information: updateDavid Wheeler — 2004
• SMART: a web-based tool for the study of genetically mobile domainsJ. Schultz — 2000
• Hidden Markov models for detecting remote protein homologiesKevin Karplus, Curtis L. Barrett, Richard Hughey — 1998
• Threading with explicit models for evolutionary conservation of structure and sequenceAnna R. Panchenko, Aron Marchler‐Bauer, Stephen H. Bryant — 1999
• Profile hidden Markov modelsSean R. Eddy — 1998
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.Stephen F. Altschul — 1997
• The crystal structure of DNA mismatch repair protein MutS binding to a G·T mismatchMeindert H. Lamers, Anastassis Perrakis, Jacqueline H. Enzlin — 2000
• Threading with explicit models for evolutionary conservation of structure and sequenceAnna Panchenko, Aron Marchler‐Bauer, Stephen H. Bryant — 1999
• Database resources of the National Center for Biotechnology InformationDavid Wheeler — 2001

Cited by

• Characteristics and prediction of domain linker sequences in multi-domain proteinsTakanori Tanaka, Yutaka Kuroda, Shigeyuki Yokoyama — 2004
• Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary ChangeGary Xie, Nemat O. Keyhani, Carol A. Bonner — 2003
• Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models敬久 出島 — 2004
• JY-1, an oocyte-specific gene, regulates granulosa cell function and early embryonic development in cattleAlfredo Hidalgo Lavié — 2007
• Detecting atypical examples of known domain types by sequence similarity searching: the SBASE domain library approach.孟紀 江本, 香織 江國, 章二 山藤 — 2010
• Immunome database for marsupials and monotremesLuis Ruiz Arbeloa — 2011
• De novo transcriptome analysis of the Siberian apricot (Prunus sibirica L.) and search for potential SSR markers by 454 pyrosequencing.闫慧兰, 雷飞, 徐萍萍 — 2014
• Bioinformatic investigations in marine microbial ecologyPhilip Heller — 2014
• Population Genetic And Genomic Analysis Of Demography And Natural Selection In Anopheles Malaria VectorsJacob E. Crawford — 2012
• The functional characterization of the gene coding for O-linked β-N-acetylglucosaminidase (OGA) in Drosophila melanogasterT. Stefanelli — 2014
• Human protein function prediction : application of machine learning for integration of heterogeneous data sourcesAnna Lobley — 2010
• A Method Based on Conserved Multiple Amino Acid Properties to Predict Amino Acid Substitutions Which Maintain the Protein StructureAvinash M. Baktula — 2004
• Phylogenetic Inference for Multidomain ProteinsMaureen Stolzer — 2011
• Xenology of beta-lactamases: association of its genetic sources and putative pleiotropismH. Pinheiro — 2013
• Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes ShrinksKira S. Makarova, Marina V. Omelchenko, Elena K. Gaidamakova — 2007
• Advanced Technologies for Managing Insect PestsI. Ishaaya, Subba Reddy Palli, A. Horowitz — 2013
• Protein model construction and evaluationD. Klose — 2008
• 腐生担子菌 Coprinus cinereus のセルロース分解時に発現が誘導される遺伝子Makoto Yoshida, Yuji Nakada, Satoshi Kaneko — 2008
• Adaptation to life at high salt concentrations in archaea, bacteria, and eukaryaNina Gunde‐Cimerman, PlemenitaÅ¡, Ana, Aharon Oren — 2005
• Search for genes involved in the synthesis of poly(L-malate) in the plasmodium of Physarum polycephalumNadthanun Pinchai — 2005

Related papers

• HomologyPlot: Searching for homology to a family of proteins using a database of unique conserved patternsJ. M. R. Parker, Robert S. Hodges — 1994
• PROMALS3D web server for accurate multiple protein sequence and structure alignmentsJiao Pei, Ming Tang, Nick V. Grishin — 2008
• Large‐scale comparison of protein sequence alignment algorithms with structure alignmentsJ.M. Sauder, Jonathan W. Arthur, Roland L. Dunbrack — 2000
• SnS-Align: a graphic tool for alignment of distantly related proteinsGaniraju C. Manyam, Ancha Baranova, Mikhail Skoblov — 2009
• Biologically relevant multiple sequence alignmentHyrum Carroll — 2008
• GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamiliesMeenakshi Iyer, Kartik Bhargava, Pavalam Murugavel — 2019
• Pairwise sequence alignment algorithms: a surveyWaqar Haque, Alex Aravind, Bharath Reddy — 2009
• A structure-based method for protein sequence alignmentMaricel G. Kann, P. A. Thiessen, Anna R. Panchenko — 2005
• PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliabilityMindaugas Margelevičius, Česlovas Venclovas — 2005
• NdPASA: A novel pairwise protein sequence alignment algorithm that incorporates neighbor‐dependent amino acid propensitiesJunwen Wang, Jin‐An Feng — 2004