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Sample search results for: abc protein superfamilies

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1 news and views 918 nature structural biology volume 8 number 11 november 2001
 

Summary:  five-fold symmetry7. These proteins were initially considered to belong to distinct superfamilies... - ties. For example, 25% of enzyme superfamilies contain proteins that carry out unrelated functions... of a protein domain's superfamily may suggest possible ...

  

Source: Lichtarge, Olivier - Department of Molecular and Human Genetics, Baylor College of Medicine

 

Collection: Biotechnology ; Biology and Medicine

 
2 ATP-binding cassette protein E is involved in gene transcription and translation in Caenorhabditis elegans
 

Summary:  Received 5 August 2004 Available online 27 August 2004 Abstract ATP-binding cassette protein E (ABCE) gene... against ABCE resulted in embryonic lethality and slow growth. These data suggest that ABCE protein might... elegans; Protein translation; Gene transcription ...

  

Source: Baillie, David - Department of Molecular Biology and Biochemistry, Simon Fraser University

 

Collection: Biology and Medicine

 
3 Protein family classification and functional annotation Cathy H. Wu *, Hongzhan Huang, Lai-Su L. Yeh, Winona C. Barker
 

Summary:  into a hierarchical order to reflect their evolutionary relation- ships. Proteins are assigned to the same superfamily... be based on both global (whole protein, e.g. PIR superfamily) and local (domain and motif) sequence... ABC chain A superfamily. We look for ...

  

Source: Georgetown University Medical Center, Protein Information Resource (PIR)

 

Collection: Biology and Medicine

 
4 Comprehensive Superfamily and Function Classification of Protein Sequences
 

Summary:  Comprehensive Superfamily and Function Classification of Protein Sequences Huang, H., Barker, W... on the basis of end-to-end similarity and domain architecture. The protein superfamily organization of the PIR... .C., Yeh, L.S., and Wu, C.H. Protein Information Resource, National ...

  

Source: Georgetown University Medical Center, Protein Information Resource (PIR)

 

Collection: Biology and Medicine

 
5 Rim 3F4 Hybridoma Cell Line This is an antibody and epitope for the development of protein expression and
 

Summary:  Segments Is a Member of the ABC Transporter Superfamily. Vol 272 (15) I April 11. 10303-10310. J. Biol... Rim 3F4 Hybridoma Cell Line This is an antibody and epitope for the development of protein... . · The Rim 3F4 antibody can be used to detect 3F4-tagged proteins by immunocytochemical methods (for example

  

Source: Michelson, David G. - Department of Electrical and Computer Engineering, University of British Columbia

 

Collection: Engineering

 
6 ABC transporters: 1, 2 or 4 substrate-binding Tiemen van der Heide and Bert Poolman
 

Summary:  receptor/translocator proteins have been found in only two families of the ABC superfamily, and the systems... to the cytoplasmic membrane (2), Chimeric receptor/translocator proteins The ABC transporter for glycine betaine from... ). Together with the ATPase subunit (OpuAA) the chimeric ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
7 Superfamily System for Functional Classification of Protein Sequences: Recognizing Cellular
 

Summary:  Superfamily System for Functional Classification of Protein Sequences: Recognizing Cellular... superfamily organization of the PIR-International Protein Sequence Database (PIR-PSD) is the only... Phosphoesterases in Sequenced Genomes W. C. Barker, H. Huang, L.S. Yeh, and C.H. Wu Protein ...

  

Source: Georgetown University Medical Center, Protein Information Resource (PIR)

 

Collection: Biology and Medicine

 
8 Graph Theoretical Insights into Evolution of Multidomain Proteins
 

Summary:  , CA then we cannot construct a Dollo parsimony tree without introducing an ancestral protein ABC... into overlapping sets of proteins called superfamilies. Each domain defines one superfamily, namely the set of all... one superfamily, proteins ...

  

Source: Batzoglou, Serafim - Department of Computer Science, Stanford University; Durand, Dannie - Departments of Computer Science & Biological Sciences, Carnegie Mellon University

 

Collection: Biology and Medicine ; Biotechnology ; Computer Technologies and Information Sciences

 
9 Graph Theoretical Insights into Evolution of Multidomain Proteins
 

Summary:  introducing an ancestral protein ABC. This property is equivalent to the Helly property, named after... divide the protein universe into overlapping sets of proteins called superfamilies. Each domain defines... proteins containing the kinase domain form one ...

  

Source: Przytycka, Teresa - Algorithms and Graph Theory for Computational /Systems Biology, NCBI

 

Collection: Environmental Sciences and Ecology ; Biology and Medicine

 
10 Chapter 1 An introduction to adenine nucleotidebinding proteins Adenosine triphosphate
 

Summary:  binding cassette (ABC) transport ATPases has been the focus of this thesis and these proteins... of an electrochemical ion gradient [19]. The class of ABC transporters is the largest (super)family within... ]. ASCE proteins ASCE (additional strand conserved ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
11 General Introduction Chapter 1: General Introduction
 

Summary:  -hydrolysis (Fig. 1c). These proteins are members of the ATP-binding cassette (ABC) superfamily of transport... and TREMBL databases, and none of the solute- binding proteins from members of the ABC superfamily [171... of the ABC ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
12 Population statistics of protein structures: lessons from structural classifications
 

Summary:  Species PDB/ reference Family Protein Class 405 1599 880 4 CATH Root Topology 652 Homologous superfamily... are called `superfamilies'. If proteins share a common fold and show some evidence of homology of a degree... Numberoffolds Distribution of superfamilies in each fold. Most ...

  

Source: Brenner, Steven E. - Department of Plant and Microbial Biology, University of California at Berkeley

 

Collection: Biotechnology

 
13 A survey of integral a-helical membrane proteins Libusha Kelly Ursula Pieper Narayanan Eswar
 

Summary:  Membrane proteins Á Superfamily analysis Á Multidrug resistance Á ABC transporters Á Target selection... ABC transporter superfamily, locating sets of multidrug resistance-associ- ated membrane proteins... domains of the human ABC transporter ...

  

Source: Sali, Andrej - Department of Biochemistry and Biophysics, University of California at San Francisco

 

Collection: Biology and Medicine ; Biotechnology

 
14 Ribosome recycling depends on a mechanistic link between the FeS cluster domain and a
 

Summary:  and regulate protein synthesis. Among them, several ATP-binding cassette (ABC) ATPases have been identified (3... ). ABC enzymes repre- sent a large protein family with members in all phyla of life. Most of them... ). Despite their large functional diversity, ABC ...

  

Source: Bedwell, David M. - Department of Microbiology, University of Alabama at Birmingham

 

Collection: Biology and Medicine

 
15 Genome Biology 2004, 5:R15 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation
 

Summary:  life. Mechanistically, this may result from the broad substrate specificity of some ABC proteins, which... are distributed across separate proteins that must then assemble in the membrane. ABC transporters are collec... to newly discovered C. elegans ABC proteins on ...

  

Source: Baillie, David - Department of Molecular Biology and Biochemistry, Simon Fraser University

 

Collection: Biology and Medicine

 
16 BIOINFORMATICS ORIGINAL PAPER Vol. 21 no. 7 2005, pages 9931001
 

Summary:  superfamilies (or other such groupings) that occur frequently in interacting protein pairs within some large... . A simple model of contacts between protein domains is used to assign a score to superfamily pairs... proteins. Rather than comparing scores for different ...

  

Source: Babu, M. Madan - Laboratory of Molecular Biology, MRC; Teichmann, Sarah - Laboratory of Molecular Biology, MRC

 

Collection: Biology and Medicine ; Biotechnology

 
17 PROTEIN INTERACTIONS AND DISEASE PHENOTYPES IN THE ABC TRANSPORTER SUPERFAMILY
 

Summary:  PROTEIN INTERACTIONS AND DISEASE PHENOTYPES IN THE ABC TRANSPORTER SUPERFAMILY LIBUSHA KELLY1... Francisco, CA 94158, USA. ABC transporter proteins couple the energy of ATP binding and hydrolysis... interfaces using crystallographic structures of isolated and complexed domains in ...

  

Source: Sali, Andrej - Department of Biochemistry and Biophysics, University of California at San Francisco

 

Collection: Biology and Medicine ; Biotechnology

 
18 Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies
 

Summary:  a superfamily, we define a family as a set of proteins that perform the same overall catalytic reaction... for 42 superfamilies from the Structural Classification of Proteins (SCOP) database [32]. These superfam... not represented is the membrane proteins class. The enzymes in these 42 ...

  

Source: Sali, Andrej - Department of Biochemistry and Biophysics, University of California at San Francisco

 

Collection: Biology and Medicine ; Biotechnology

 
19 Functional Neighbors: Inferring Relationships between Non-Homologous Protein Families Using Family-Specific Packing Motifs
 

Summary:  in all representative protein structures, and (3) report those SCOP (super)families in which a particular... /NAD(P)-binding domain proteins. We used value 15/43. No new significantly enriched (super)families were discovered... in a protein from the FAD/NAD binding domain ...

  

Source: Huan, Jun "Luke" - Information and Telecommunication Technology Center & Department of Electrical Engineering and Computer Science, University of Kansas; Prins, Jan - Department of Computer Science, University of North Carolina at Chapel Hill; Wang, Wei - Department of Computer Science, University of North Carolina at Chapel Hill

 

Collection: Biology and Medicine ; Computer Technologies and Information Sciences

 
20 The SUPERFAMILY database in 2007: families and functions
 

Summary:  The SUPERFAMILY database provides protein domain assignments, at the SCOP `superfamily' level, for the predicted... protein sequences in over 400 completed genomes. A superfamily groups together domains of different... -level functional annotation. The SUPERFAMILY ...

  

Source: Vogel, Christine - Institute for Cellular and Molecular Biology, University of Texas at Austin

 

Collection: Biotechnology ; Biology and Medicine


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21 ABC transporters ABC transporter architecture and regulatory roles of
 

Summary:  -binding proteins (SBPs) of ABC uptake systems that reside in the periplasmic space of Gram-negative bacteria, from... superfamily. They contain the ATP-binding cassettes, hence the name ABC transporters. Many crystal structures... and not restricted to ABC proteins ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
22 Length Variations amongst Protein Domain Superfamilies and Consequences on Structure and
 

Summary:  Length Variations amongst Protein Domain Superfamilies and Consequences on Structure and Function... , India Abstract Background: Related protein domains of a superfamily can be specified by proteins... -domain proteins involving interactions with domains from the same ...

  

Source: Srinivasan, N. - Molecular Biophysics Unit, Indian Institute of Science, Bangalore

 

Collection: Biology and Medicine

 
23 The SUPERFAMILY database in 2007: families and functions
 

Summary:  ABSTRACT 10 The SUPERFAMILY database provides protein domain assignments, at the SCOP `superfamily' level... , for the predicted protein sequences in over 400 completed genomes. A superfamily groups together domains... for general protein evolution and ...

  

Source: Gough, Julian - RIKEN Genomic Sciences Centre

 

Collection: Biotechnology

 
24 Introduction General introduction
 

Summary:  others including ATPases of the ABC transporter superfamily, the F-ATPase superfamily or the motor... ATPases of the General Secretory (Sec) pathway. Motor proteins from these superfamilies show a low... ; amongst others including ATPases of the ABC transporter ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
25 nature structural biology volume 8 number 11 november 2001 953 Identification of
 

Summary:  map of folds in protein space and then further subdividing fold neighborhoods into superfamilies based... . Thus, superfamilies can be delineated as con- tinuous neighborhoods in the map of protein space (Fig. 1... . In the resulting map of protein space, ...

  

Source: Pilpel, Yitzhak - Department of Molecular Genetics, Weizmann Institute of Science

 

Collection: Biology and Medicine

 
26 UNIVERSITY OF LEEDS Statistical methods for matching
 

Summary:  in predicting "off-target liabilities" in drug design studies by calculating enrichment of protein superfamilies... of highly similar domains. Protein families are clustered together into superfamilies that share some... . . . . . . . . . . . . . . . . . . . . . . . . . . 124 5.6 Distribution of ...

  

Source: Haase, Markus - Elektrotechniek, Wiskunde en Informatica, Technische Universiteit Delft

 

Collection: Mathematics

 
27 BioMed Central Page 1 of 14
 

Summary:  variations that could be as much as two-fold in some protein superfamilies. In this paper, we describe... superfamily alignments from PASS2, we find that 'length- deviant' protein superfamilies show > 30% length... of different lengths even within a single protein ...

  

Source: Srinivasan, N. - Molecular Biophysics Unit, Indian Institute of Science, Bangalore

 

Collection: Biology and Medicine

 
28 General introduction I. General features of cell volume control
 

Summary:  the whole ABC-superfamily. In this respect, it is of interest to consider also the solute efflux proteins, e... to an osmotic upshift are substrate-binding protein-dependent ABC transporters, which use ATP as source... shown that a subset of ABC transporters has the ligand- binding ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
29 Proteins: Structure, Function, and Genetics Article No. 7e0847
 

Summary:  structures. In contrast, a superfamily is a subset of the fold, denoting groups of proteins that have closer... superfamily is the EGF/ Laminin, both mostly present in extracellular, often highly repetitious proteins... superfamily (7.38.1) was also identified in several human ...

  

Source: Gerstein, Mark - Department of Molecular Biophysics and Biochemistry, Yale University

 

Collection: Biology and Medicine ; Biotechnology

 
30 Statistical Applications in Genetics and Molecular Biology
 

Summary:  of the constituent do- mains within proteins, scoring pairs of domain superfamilies according to their propensity... into a superfamily, and the constituent superfamilies within a protein can be identified from the protein sequence... are known, the ...

  

Source: Babu, M. Madan - Laboratory of Molecular Biology, MRC; Teichmann, Sarah - Laboratory of Molecular Biology, MRC

 

Collection: Biology and Medicine ; Biotechnology

 
31 Ways & Means 1087 CAMPASS: a database of structurally aligned protein
 

Summary:  Ways & Means 1087 CAMPASS: a database of structurally aligned protein superfamilies R Sowdhamini... of superfamilies that include previously identified members of known function and even proteins of known three... of superfamily alignments (CAMPASS, CAM- bridge database of ...

  

Source: Srinivasan, N. - Molecular Biophysics Unit, Indian Institute of Science, Bangalore

 

Collection: Biology and Medicine

 
32 Proc. Natl. Acad. Sci. USA Vol. 95, pp. 14658 --14663, December 1998
 

Summary:  MG sequences are members of protein families. Table 3. Functions of large superfamilies formed... assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements... step toward determining the families of protein domains that form the products of these genes, we ...

  

Source: Teichmann, Sarah - Laboratory of Molecular Biology, MRC

 

Collection: Biotechnology ; Biology and Medicine

 
33 Proc. Natl. Acad. Sci. USA Vol. 95, pp. 1465814663, December 1998
 

Summary:  assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements... step toward determining the families of protein domains that form the products of these genes, we have... products of M. genitalium to the sequences of the domains that form proteins of known structure ...

  

Source: Teichmann, Sarah - Laboratory of Molecular Biology, MRC

 

Collection: Biotechnology ; Biology and Medicine

 
34 A PROPOSAL FOR THE PIRSF (PIR SUPERFAMILY) CLASSIFICATION SYSTEM
 

Summary:  A PROPOSAL FOR THE PIRSF (PIR SUPERFAMILY) CLASSIFICATION SYSTEM May 30, 2003 Protein Information... ............................................................................................................ 9 #12;1 A. Introduction ­ A Brief History The concept of protein superfamilies was articulated... ...

  

Source: Georgetown University Medical Center, Protein Information Resource (PIR)

 

Collection: Biology and Medicine

 
35 between metabolic diversity and the associated regulatory cost that maximally exploits the environment while
 

Summary:  .A.G. et al. (2004) Evolution of protein superfamilies and bacterial genome size. J. Mol. Biol. 336, 871... to the sequential arrangement of domains within a protein as assigned by the SUPERFAMILY procedure as the domain... ­540 9 Gough, J. and Chothia, C. (2002) SUPERFAMILY:HMMs ...

  

Source: Teichmann, Sarah - Laboratory of Molecular Biology, MRC

 

Collection: Biotechnology ; Biology and Medicine

 
36 Functional hot spots in human ATP-binding cassette transporter
 

Summary:  (ABC) transporter superfamily consists of 48 integral membrane proteins that couple the action of ATP... the functional effects of nsSNPs in this clinically important membrane transporter superfamily. Keywords: ABC... (PDB) with the Struc- tural Classification of ...

  

Source: Sali, Andrej - Department of Biochemistry and Biophysics, University of California at San Francisco

 

Collection: Biology and Medicine ; Biotechnology

 
37 PIR and iProClass for Functional Genomics/Proteomics Barker, W.C., Castro-Alvear, J., Chen, Y., Hu, Z., Huang, H., Ledley, R.S., Lewis, K.C.,
 

Summary:  as structural/functional classifications and features of proteins. The PIR superfamily/family organization... -redundant PIR and SwissProt proteins organized with more than 30,000 superfamilies, 100,000 families, 3000... sequences. Protein and superfamily summary ...

  

Source: Georgetown University Medical Center, Protein Information Resource (PIR)

 

Collection: Biology and Medicine

 
38 Protein Family Expansions and Biological Christine Vogel1,2*
 

Summary:  in terms of the number of proteins that contain domains of defined superfamilies [16] (Figure 1B... , and function [16]. Two proteins that contain a domain of the same superfamily are grouped into one protein... Superfamilies as Units of Protein ...

  

Source: Vogel, Christine - Institute for Cellular and Molecular Biology, University of Texas at Austin

 

Collection: Biotechnology ; Biology and Medicine

 
39 Protein Family Expansions and Biological Christine Vogel1,2*
 

Summary:  of proteins that contain domains of defined superfamilies [16] (Figure 1B and Dataset S1). Domains... into superfamilies based on evidence from structure, sequence, and function [16]. Two proteins that contain a domain... of the same superfamily are grouped into one ...

  

Source: Vogel, Christine - Institute for Cellular and Molecular Biology, University of Texas at Austin

 

Collection: Biotechnology ; Biology and Medicine

 
40 DOMAIN SUPERFAMILY EXPANSIONS SUPPORTING MATERIAL 1 SUPPORTING INFORMATION --
 

Summary:  DOMAIN SUPERFAMILY EXPANSIONS ­ SUPPORTING MATERIAL 1 Vogel, C. SUPPORTING INFORMATION -- PROTEIN... . This is because most proteins contain only one instance of a particular domain superfamily. b) Our analysis... proteins, is the result of balancing between including as many ...

  

Source: Vogel, Christine - Institute for Cellular and Molecular Biology, University of Texas at Austin

 

Collection: Biotechnology ; Biology and Medicine


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41 Vol. 22 no. 23 2006, pages 28762882 doi:10.1093/bioinformatics/btl490BIOINFORMATICS ORIGINAL PAPER
 

Summary:  may include either the correct homooligomer or interactions with proteins of other superfamilies... of two protein superfamilies or families as defined by the SCOP database (Murzin et al., 1995... Structural bioinformatics ProtBuD: a database of biological unit structures of protein ...

  

Source: Obradovic, Zoran - Center for Information Science and Technology & Department of Computer and Information Sciences, Temple University

 

Collection: Computer Technologies and Information Sciences

 
42 Introduction to multidrug transporters, cellular resistance and lantibiotic production in Lactococcus lactis
 

Summary:  the cytoplasmic membrane. Many MDR transporters are members of the large ATP-binding cassette (ABC) superfamily (2... (RND) superfamily. These are proton motive force driven transporters that are part of a larger protein... .1. Schematic representation of the major protein ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
43 iProClass: An Integrated Protein Classification Database for Wu, C. H., Chen, Y., Huang, H., Barker, W.C.
 

Summary:  /site) levels, as well as structural/functional classifications and features of proteins. The PIR superfamily... than 266,000 non- redundant PIR and Swiss-Prot proteins organized with more than 30,000 superfamilies... . Protein and superfamily summary reports provide ...

  

Source: Georgetown University Medical Center, Protein Information Resource (PIR)

 

Collection: Biology and Medicine

 
44 Published online 13 November 2007 Nucleic Acids Research, 2008, Vol. 36, Database issue D419D425 doi:10.1093/nar/gkm993
 

Summary:  , on the rates of discovery and growth of protein families and superfamilies. SCOP can be accessed at http... with related sequences but typically distinct functions; and Superfamily bridging together protein families... , accumulating many more new families and proteins. The division of ...

  

Source: Brenner, Steven E. - Department of Plant and Microbial Biology, University of California at Berkeley

 

Collection: Biotechnology

 
45 Interaction Interfaces of Protein Domains Are Not Topologically Equivalent Across Families Within
 

Summary:  interfaces on the tertiary folds between members of distantly related protein domain superfamilies. The data... functionality is preserved at the domain superfamily level, the effect of biochemical function on protein... assemblies is different in these protein domains related by ...

  

Source: Srinivasan, N. - Molecular Biophysics Unit, Indian Institute of Science, Bangalore

 

Collection: Biology and Medicine

 
46 Applied Mathematics Letters 24 (2011) 12511256 Contents lists available at ScienceDirect
 

Summary:  of the cells by several transporters of the ABC superfamily. The variable ABC_CPT represents transporters... the following model for mRNA and protein amounts of ABC transporters responsible for CPT11 and SN38 efflux: d[ABC... RNA) and degradation ...

  

Source: Clairambault, Jean - Biologie, Analyse Numérique, Géophysique Team, INRIA Paris-Rocquencourt

 

Collection: Biology and Medicine

 
47 BioMed Central Page 1 of 14
 

Summary:  Binding Pro- tein), and 3.30.450.20 (Signaling Protein) superfamilies. The poor performance of the SSEF... Protein) superfamily contains structural representatives of the PAS domain, a family of sensor protein... - gram [25]. (b) The 3.30.300.20 (Rna Binding Protein) ...

  

Source: O'Leary, Dianne P. - Institute for Advanced Computer Studies & Department of Computer Science, University of Maryland at College Park

 

Collection: Computer Technologies and Information Sciences

 
48 January, 2003 1 The Protein Space
 

Summary:  : P-loop Rossmann fold F: G-protein 3.40.50.300 Superfamily: P-loop containing nucleotide triphosphate... in the road-map belong to the same superfamily (SCOP - NAT) The road-map connect proteins that are considered... January, 2003 1 The Protein Space From Sequence to Structure to ...

  

Source: Linial, Michal - Sudarsky Center for Computational Biology & Department of Biological Chemistry, Hebrew University of Jerusalem

 

Collection: Biology and Medicine

 
49 Discussion and concluding remarks General introduction
 

Summary:  and reaction-stoichiometry of ABC transporters In vivo studies on substrate-binding protein- dependent ABC... bidirectional solute movement might be a general feature of the transport members of the ABC-superfamily... for the catalytic mechanism of substrate-binding protein- dependent ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
50 Cell, Vol. 93, 951960, June 12, 1998, Copyright 1998 by Cell Press The C. elegans Cell Corpse
 

Summary:  transporters. Like other members of the ABC trans- porter superfamily, the CED-7 protein has two NBDs... (ABC) protein superfamily. EMBO J. 10, 3777­3785. #12;C. elegans CED-7 Is Similar to ABC Transporters... Engulfment Gene ced-7 Encodes a ...

  

Source: Horvitz, H. Robert - Department of Biology, Massachusetts Institute of Technology (MIT)

 

Collection: Biology and Medicine

 
51 Update on human genome completion and annotations: Protein information
 

Summary:  Prot--the Universal Protein Resource--which now unifies the PIR, Swiss-Prot and TrEMBL databases. The PIRSF (SuperFamily... EMBL. To facilitate consistent and accurate protein annotation, PIR has extended its superfamily concept and developed... -PSD, SwissProt and TrEMBL) ...

  

Source: Georgetown University Medical Center, Protein Information Resource (PIR)

 

Collection: Biology and Medicine

 
52 Annotation Transfer for Genomics: Measuring Functional Divergence
 

Summary:  present a large-scale survey of annotation transfer in these proteins, using scop superfamilies to define... of proteins sharing one structural superfamily. In contrast, this value is 67% for pairs of single... -domain proteins sharing the same structural superfamily. ...

  

Source: Gerstein, Mark - Department of Molecular Biophysics and Biochemistry, Yale University

 

Collection: Biology and Medicine ; Biotechnology

 
53 The SUPERFAMILY database in 2004: additions and improvements
 

Summary:  ABSTRACT The SUPERFAMILY database provides structural assignments to protein sequences and a framework... . The SUPERFAMILY database is based on the SCOP classi®cation of protein domains (3). SCOP de®nes domains... of SUPERFAMILY is to identify within protein ...

  

Source: Gough, Julian - RIKEN Genomic Sciences Centre; Vogel, Christine - Institute for Cellular and Molecular Biology, University of Texas at Austin

 

Collection: Biology and Medicine ; Biotechnology

 
54 electronic reprint Acta Crystallographica Section D
 

Summary:  rights reserved The SUPERFAMILY hidden Markov model library repre- senting all proteins of known... structure predicts the domain architecture of protein sequences and classi®es them at the SCOP superfamily... at http://supfam.org. 2.1. What it does The purpose of SUPERFAMILY is to ...

  

Source: Gough, Julian - RIKEN Genomic Sciences Centre

 

Collection: Biotechnology

 
55 Function of prokaryotic and eukaryotic ABC proteins in lipid transport Antje Pohla,b
 

Summary:  Elsevier B.V. All rights reserved. Keywords: ABC protein superfamily; Flippase; Cholesterol; Lipid... the transbilayer distribution of endogenous lipids. 3. General features of the ABC protein superfamily The ATP... -binding cassette (ABC) ...

  

Source: Institut de Biologie Physico-Chimique CNRS, Physico-Chimie Moléculaire des Membranes Biologiques

 

Collection: Chemistry ; Biology and Medicine

 
56 1371 PROTEIN STRUCTURE INTERPRETATION WITH SCOP 635 gram MULTISUP,32 which performs weighted multiple superposition of
 

Summary:  and structure. Superfamilies consist of families whose proteins share very common structure and function... , these proteins cannot be classified as having the same fold or superfamily (seebelow). Topological similaritiesof... additional levels of classi- fication to make such distinctions explicit. ...

  

Source: Brenner, Steven E. - Department of Plant and Microbial Biology, University of California at Berkeley

 

Collection: Biotechnology

 
57 Protein Structure Analysis Iosif Vaisman
 

Summary:  of Proteins CATH - Class, architecture, topology and homologous superfamily SCOP: Structural Classification... sequence identities of only 15%. #12;SCOP: Structural Classification of Proteins Superfamily: Probable... in superfamilies. For example, actin, the ATPase domain of the heat ...

  

Source: Vaisman, Iosif - Bioinformatics and Computational Biology Program, School of Computational Sciences, George Mason University

 

Collection: Biotechnology

 
58 Superfamily Assignments for the Yeast Proteome through Integration of Structure
 

Summary:  superfamilies. This relationship can be exploited when predicting to which structure superfamily a protein... belongs [9]. We describe an integrated approach for assigning protein domains to structure superfamilies... structure comparison program [21]. The reliability of an assignment to ...

  

Source: Baker, David - Center for Nanotechnology and NanoTechnology & Department of Biochemistry, University of Washington at Seattle

 

Collection: Chemistry ; Biotechnology

 
59 Superfamily Assignments for the Yeast Proteome through Integration of Structure
 

Summary:  superfamilies. This relationship can be exploited when predicting to which structure superfamily a protein... belongs [9]. We describe an integrated approach for assigning protein domains to structure superfamilies... structure comparison program [21]. The reliability of an assignment to ...

  

Source: Davis, Trisha N. - Department of Biochemistry, University of Washington at Seattle

 

Collection: Biology and Medicine ; Environmental Management and Restoration Technologies

 
60 NSF ITR-0205470 TECHNICAL REPORT
 

Summary:  superfamily" be tagged, since it refers to a family of proteins. 2.5.4.2 Relations between different protein... " or "Ca2(+)-activated actin-binding protein" (PMID-1847147). Similarly, "ABC protein-mediated exporters... NSF ITR-0205470 TECHNICAL REPORT Guidelines for ...

  

Source: Georgetown University Medical Center, Protein Information Resource (PIR)

 

Collection: Biology and Medicine


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61 Genomic scale sub-family assignment of protein domains
 

Summary:  superfamilies containing 2845 unevenly distributed families including 10 894 proteins with sequences... in multi- domain proteins via splicing. We also observe that some superfamilies have several or many... ,K. (1998) Phylogenetic inference in protein superfamilies: ...

  

Source: Gough, Julian - RIKEN Genomic Sciences Centre

 

Collection: Biotechnology

 
62 Critical Review Structural and Functional Characterization of Gene Products Encoded
 

Summary:  or proteins one each from these superfamilies could provide templates for inter- preting the functions... genome is discussed further. Patched-like Transport Protein Superfamily This superfamily consists... -like activity. DISTRIBUTION OF PROTEIN DOMAIN FOLDS AND ...

  

Source: Srinivasan, N. - Molecular Biophysics Unit, Indian Institute of Science, Bangalore

 

Collection: Biology and Medicine

 
63 Structure, function and evolution of multidomain proteins Christine Vogel
 

Summary:  . In this review, we discuss how domain superfamilies form the repertoire of multidomain proteins via duplication... of multidomain proteins: the repertoire of domain superfamilies and their role in the formation of multidomain... , homodimeric transcriptional repressors of the Iron-dependent repressor ...

  

Source: Teichmann, Sarah - Laboratory of Molecular Biology, MRC; Vogel, Christine - Institute for Cellular and Molecular Biology, University of Texas at Austin

 

Collection: Biology and Medicine ; Biotechnology

 
64 Journal of Bioinformatics and Computational Biology c Imperial College Press
 

Summary:  hypothesis, we first determine if the protein belongs to an existing category (family, superfamily, fold... of protein sequences at the family, superfamily, and fold levels11 . They observed that the best- attained... . Does this protein belong to an existing category ...

  

Source: California at Santa Barbara, University of - Department of Computer Science, Bioinformatics Research Group

 

Collection: Computer Technologies and Information Sciences

 
65 Use of Text Mining for Protein Structure Prediction and Functional Annotation in Lack of Sequence Homology
 

Summary:  Use of Text Mining for Protein Structure Prediction and Functional Annotation in Lack of Sequence... relationships even if there is little or no sequence homology between the compared proteins, the difficult... that uses literature to assist SCOP super-family prediction [2] significantly improves on our original ab

  

Source: Rocha, Luis - School of Informatics, Indiana University

 

Collection: Computer Technologies and Information Sciences

 
66 Chapter 3 Enrichment of adenine nucleotidebinding proteins using the ATPbased nucleotide analogues
 

Summary:  of adeninenucleotide binding proteins is described in this chapter. Several overproduced ABC transporters... of ABC (transport) proteins The use of the ATP analog BHacATP did identify multiple adenine... of the family of ABC (transport) proteins. ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
67 Joint learning of logic relationships for studying protein function using phylogenetic profiles and the
 

Summary:  membrane protein ABC transporter. This hypothesis is supported by a FASTA score 6 which infers that Ugp... , the superfamily II Helicase, associated with COG1204, is connected to ABC- type antimicrobial peptide transport... pathway. COG3845 is clustered with proteins whose function in the ...

  

Source: Baral, Chitta - Department of Computer Science and Engineering, Arizona State University

 

Collection: Computer Technologies and Information Sciences

 
68 General Introduction General Introduction
 

Summary:  superfamily of primary transporters are the ATP-binding cassette (ABC) transporters (Fig. 1; Higgins, 1992... (Pao et al., 1998). The ABC and MF superfamilies constitute the two most abundant and widely spread... of membrane proteins, amongst which the oligopeptide ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
69 Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies
 

Summary:  coverage of the amidohy- drolase and enolase superfamilies. Using sequence- and structure-based protein... superfamilies. Next, we determine the number of protein sequences in the comprehensive sequence databases... superfamily, since these proteins bind only a ...

  

Source: Sali, Andrej - Department of Biochemistry and Biophysics, University of California at San Francisco

 

Collection: Biology and Medicine ; Biotechnology

 
70 TAT-Pathway-Dependent Lipoproteins as a Niche-Based Adaptation in Prokaryotes
 

Summary:  and big genomes (Fig. 5). Out of the 562 transporters/binding proteins, 194 are components of ABC... include extracellular solute-binding proteins Enzymes, 503, 22% Superfamily unassigned hypothetical... proteins, 228, 10% Transporters and Binding proteins, 562, 24% ...

  

Source: Babu, M. Madan - Laboratory of Molecular Biology, MRC

 

Collection: Biotechnology

 
71 Copyright 2007 by the Genetics Society of America DOI: 10.1534/genetics.106.066720
 

Summary:  -binding cassette (ABC) transporter proteins con- stitute one of the largest protein families in both prokaryotes... acids into the cell. In eukaryotes, the majority of ABC transporter proteins are involved in exporting... -binding proteins, and an ...

  

Source: Baillie, David - Department of Molecular Biology and Biochemistry, Simon Fraser University

 

Collection: Biology and Medicine

 
72 January 29, 2004 2:46 WSPC/Trim Size: 9in x 6in for Review Volume practicalbioinformatician A FAMILY CLASSIFICATION APPROACH TO FUNCTIONAL
 

Summary:  families of proteins, such as the superfamilies/families 62 in the PIR­PSD, and protein groups in Proto... of these, the protein­to­family relationship is not necessarily one­to­one, as in PIR superfamily... protein, e.g., PIR superfamily) ...

  

Source: Wong, Limsoon - Department of Computational Science, National University of Singapore

 

Collection: Computer Technologies and Information Sciences

 
73 A Novel 3D Shape-Based Indexing Scheme for the CATH Protein Structure Classification
 

Summary:  oprotein structures according to their CATH superfamilies. The same six proteins chains from the expansion... A Novel 3D Shape-Based Indexing Scheme for the CATH Protein Structure Classification Lazaros... sequence-independent protein structure alignment, comparison, and classification (Mavridis and Ritchie ...

  

Source: Ritchie, Dave - INRIA & Laboratoire Lorrain de Recherche en Informatique et ses Applications (Loria), Université Henri Poincaré -Nancy-Université

 

Collection: Biology and Medicine ; Computer Technologies and Information Sciences

 
74 Sugar Transport in (Hyper-)Thermophilic Archaea Sonja M. Koning, Sonja-Verena Albers, Wil N. Konings and Arnold J. M.
 

Summary:  ;Introduction 4 2.2. Binding protein dependent ABC- type transporters The sugar transporters characterized so... the ABC-signature motif LSGGQ (Boos and Shuman, 1998). The ATP-binding proteins of the trehalose... , and Rad50cd, a DNA repair protein which shows ATP-binding domains similar ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
75 Tandem Clusters of Membrane Proteins in Complete Genome Sequences
 

Summary:  of isolated ATP-binding protein components in the ABC transporters. Possible implications of tandem cluster... transporters, and the rest. The membrane proteins of ABC transporters (Fig. 2A) exhibit the most characteristic... in Figure 2A. The membrane proteins for the transporters other ...

  

Source: Kihara, Daisuke - Department of Biological Sciences, Purdue University

 

Collection: Biology and Medicine ; Biotechnology

 
76 January 29, 2004 2:46 WSPC/Trim Size: 9in x 6in for Review Volume practical-bioinformatician A FAMILY CLASSIFICATION APPROACH TO FUNCTIONAL
 

Summary:  families of proteins, such as the superfamilies/families ¾ in the PIR-PSD, and protein groups in Proto... assignments, protein identifications must be based on both global (whole protein, e.g., PIR superfamily... , the related superfamilies are: ...

  

Source: Wong, Limsoon - Department of Computational Science, National University of Singapore

 

Collection: Computer Technologies and Information Sciences

 
77 proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Protein structure mining using
 

Summary:  local and GA techniques to extract structurally similar proteins at class, fold, super-family... . Table I reports efficiency rate for mining proteins at class, fold, super-family, and family level... protein. Table III summarizes the results obtained for each level, mainly class, fold, ...

  

Source: Srinivasan, N. - Molecular Biophysics Unit, Indian Institute of Science, Bangalore

 

Collection: Biology and Medicine

 
78 Novel motifs in amino acid permease genes from Leishmania Martin Akermana,1
 

Summary:  to the amino acid transporter-1 and one to the amino acid polya- mino-choline superfamilies. Using... in these proteins might be useful to better understand parasite physiology within its hosts. Ó 2004 Elsevier Inc... in numerous processes such as protein synthesis, energy and nitrogen metabolism, osmoregulation, hormone

  

Source: Mandel-Gutfreund, Yael - Department of Biology, Technion, Israel Institute of Technology

 

Collection: Biology and Medicine

 
79 The ASTRAL Compendium in 2004 John-Marc Chandonia1
 

Summary:  ABSTRACT The ASTRAL Compendium provides several data- bases and tools to aid in the analysis of protein... of protein structure domains, it includes sequences for each domain and other resources useful for studying... and automated methods. ASTRAL may be accessed at http://astral.stanford. edu/. BACKGROUND The Protein Data Bank

  

Source: Brenner, Steven E. - Department of Plant and Microbial Biology, University of California at Berkeley; California at Davis, University of - Computer Science Department, Computer Science Theory Laboratory; Levitt, Michael - Department of Structural Biology, Stanford University

 

Collection: Biology and Medicine ; Biotechnology ; Computer Technologies and Information Sciences

 
80 1997 Oxford University Press 16651677Nucleic Acids Research, 1997, Vol. 25, No. 9 Extracting protein alignment models from the
 

Summary:  Sen1 protein early on constructs a superfamily I helicase (40) model containing seven conserved... of the glycosyltrans- ferases described below). For example, S-adenosylmethionine binding proteins, ABC transporters... , the helicase I and II superfamilies, the major facilitator and ...

  

Source: Liu, Jun - Department of Statistics, Harvard University

 

Collection: Biotechnology ; Mathematics


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81 Annotation Transfer for Genomics: Measuring Functional Divergence in Multi-Domain Proteins
 

Summary:  -scale survey of annotation transfer in these proteins, using scop superfamilies to define domain folds... structural superfamily. In contrast, this value is 67% for pairs of single-domain proteins sharing the same... structural superfamily. On the other hand, if two multi-domain ...

  

Source: Gerstein, Mark - Department of Molecular Biophysics and Biochemistry, Yale University

 

Collection: Biology and Medicine ; Biotechnology

 
82 COMMUNICATION Proteins with Class a/b Fold Have High-level
 

Summary:  genomes and subsequent struc- ture annotations to the component proteins at a SCOP superfamily level... and subsequent struc- ture annotations to the component proteins at a superfamily level with hidden Markov models... superfamilies. The SCOP domains were assigned to ...

  

Source: Gough, Julian - RIKEN Genomic Sciences Centre

 

Collection: Biotechnology

 
83 PROTEIN FOLDS IN THE WORM GENOME M. GERSTEIN, J. LIN, H. HEGYI
 

Summary:  of other superfamilies in multidomain proteins. Explanation of columns 3-6: number of times the superfamily... with 26 other types of superfamilies in multidomain proteins, 16 occurring more than once and 10 only once... superfamilies, 224 were found in single, 191 ...

  

Source: Gerstein, Mark - Department of Molecular Biophysics and Biochemistry, Yale University

 

Collection: Biology and Medicine ; Biotechnology

 
84 Bibliography Abrahams, J. and Leslie, A. (1996). Methods used in the structure determination of
 

Summary:  ., Perozo, E., and Locher, K. (2007). Asymmetry in the structure of the ABC transporter binding protein... of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory... -70. Wilkinson, A. J. (2002). Abc proteins: ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
85 Expression Analysis of ABC Transporters Reveals Differential Functions of Tandemly Duplicated Genes in
 

Summary:  these putative ABC genes work in worms, we generated promoter­fluorescent protein fusions for the entire family... Introduction ATP-binding cassette (ABC) transporters consti- tute one of the largest protein families in both... for cystic fibrosis.6 Some ABC ...

  

Source: Baillie, David - Department of Molecular Biology and Biochemistry, Simon Fraser University

 

Collection: Biology and Medicine

 
86 Clustering Chain Additional options
 

Summary:  information hidden in the roadmap ? The case of Globin superfamily #12;8 Proteins with >30% sequence identity... -map belong to the same superfamily (SCOP - NAT) The road-map connect proteins that are considered... superfamily ProTarget - an interactive web site that assign a `SCORE' ...

  

Source: Linial, Michal - Sudarsky Center for Computational Biology & Department of Biological Chemistry, Hebrew University of Jerusalem

 

Collection: Biology and Medicine

 
87 CHOP Proteins Into Structural Domain-Like Fragments Jinfeng Liu1,3,4* and Burkhard Rost1,2,3*
 

Summary:  PROTEINS INTO STRUCTURAL DOMAIN-LIKE FRAGMENTS 681 #12;Partial Agreement With SUPERFAMILY Assignments... , namely, yeast, the smallest entirely sequenced eukaryote with 6349 proteins. SUPERFAMILY assigned 4794... proteins. About 72% of the SUPERFAMILY domains are ...

  

Source: Rost, Burkhard - Department of Biochemistry and Molecular Biophysics, Columbia University

 

Collection: Biology and Medicine

 
88 The evolution of domain arrangements in proteins and interaction networks
 

Summary:  for proteins as different as ABC transporters, ribosomal proteins, histones, homeobox proteins [47... Review The evolution of domain arrangements in proteins and interaction networks E. Bornberg... Abstract. Proteins are composed of domains, which are conserved ...

  

Source: Teichmann, Sarah - Laboratory of Molecular Biology, MRC

 

Collection: Biotechnology ; Biology and Medicine

 
89 Published online 23 October 2008 Nucleic Acids Research, 2009, Vol. 37, Database issue D347D354 doi:10.1093/nar/gkn791
 

Summary:  -binding cassette (ABC) transporter superfamily. Genome Res., 11, 1156­1166. 42. Hamosh,A., Scott,A.F., Amberger... doi:10.1093/nar/gkn791 MODBASE, a database of annotated comparative protein structure models... ://salilab.org/modbase) is a data- base of annotated comparative protein structure models. The ...

  

Source: Sali, Andrej - Department of Biochemistry and Biophysics, University of California at San Francisco

 

Collection: Biology and Medicine ; Biotechnology

 
90 Nucleic Acids Research, 2008, 18 doi:10.1093/nar/gkn791
 

Summary:  comparative protein structure models and associated resources Ursula Pieper1 , Narayanan Eswar1 , Ben M. Webb1... , 2008 ABSTRACT MODBASE (http://salilab.org/modbase) is a data- base of annotated comparative protein... :/salilab.org/modeller). MODBASE currently contains 5 152 695 reliable models for domains in 1 593 209 unique ...

  

Source: Eddy, Sean - Janelia Farm Research Campus, Howard Hughes Medical Institute

 

Collection: Biology and Medicine

 
91 Published online 23 October 2008 Nucleic Acids Research, 2009, Vol. 37, Database issue D347D354 doi:10.1093/nar/gkn791
 

Summary:  -binding cassette (ABC) transporter superfamily. Genome Res., 11, 1156­1166. 42. Hamosh,A., Scott,A.F., Amberger... doi:10.1093/nar/gkn791 MODBASE, a database of annotated comparative protein structure models... ://salilab.org/modbase) is a data- base of annotated comparative protein structure models. The ...

  

Source: Eddy, Sean - Janelia Farm Research Campus, Howard Hughes Medical Institute

 

Collection: Biology and Medicine

 
92 Amidohydrolase Superfamily
 

Summary:  superfamily' has referred to a struc- tural relationship among the metal-dependent proteins that contain... ://scop.mrc-lmb.cam.ac.uk/scop), the amidohydrolase superfamily is a large `metal-dependent hydrolase' protein group under the `alpha and beta... proteins (a/b)' clan. The ...

  

Source: Correia, John J. - Department of Biochemistry, University of Mississippi

 

Collection: Biology and Medicine

 
93 Nature Macmillan Publishers Ltd 1998 letters to nature
 

Summary:  proteins', and `fatty acid and phospholipid metabolism' categories (Table 2). The superfamily of ATP... /G, osmoprotection protein; Cu2+ , copper-transporting ATPase; +?, cation-transporting ATPase; ?, ABC... P 4 3 2 pstABC cysAT nrtBC arsB cynX mae1 Iron-sulfur ...

  

Source: Badger, Jonathan - Institute for Genomic Research, Rockville

 

Collection: Biotechnology ; Biology and Medicine

 
94 ProtoMap: Automatic classi cation of protein sequences, a hierarchy of
 

Summary:  protein families and superfamilies The hierarchical organization also suggests classi#12;cation within... , as illustrated for the small G-protein/Ras superfamily (Fig. 9.3). The ras gene is a member of a family that has... to as the small-G-protein superfamily ...

  

Source: Yona, Golan - Department of Computer Science, Technion, Israel Institute of Technology

 

Collection: Computer Technologies and Information Sciences

 
95 Scaling Law in Sizes of Protein Sequence Families: From Super-Families to Orphan Genes
 

Summary:  Scaling Law in Sizes of Protein Sequence Families: From Super-Families to Orphan Genes Ron Unger,1... , there are several "super-families"3 that include many proteins and, on the other hand, there is a large number... comparisons. Curr Opin Genet Dev 1999;9:630­636. 3. Orengo CA, Jones DT, Thornton JM. ...

  

Source: Unger, Ron - Faculty of Life Sciences, Bar Ilan University

 

Collection: Biology and Medicine

 
96 Vol. 21 no. 20 2005, pages 38243831 doi:10.1093/bioinformatics/bti627BIOINFORMATICS ORIGINAL PAPER
 

Summary:  dataset. Within SCOP, related protein domains are grouped into superfamilies. There are a few large... as those within larger superfamilies. However, this is not the case. In gen- eral, proteins within small... superfamilies account for most true relations between ...

  

Source: Brenner, Steven E. - Department of Plant and Microbial Biology, University of California at Berkeley

 

Collection: Biotechnology

 
97 General Introduction General Introduction
 

Summary:  of secondary transporters. The ABC and MF superfamilies form the two largest transporter families found... family of proteins within the class of secondary transporters is the Major Facilitator Superfamily... General Introduction 1 General Introduction 1. Membrane transport proteins Cells ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
98 Vol. 21 no. 20 2005, pages 38243831 doi:10.1093/bioinformatics/bti627BIOINFORMATICS ORIGINAL PAPER
 

Summary:  dataset. Within SCOP, related protein domains are grouped into superfamilies. There are a few large... as those within larger superfamilies. However, this is not the case. In gen- eral, proteins within small... superfamilies account for most true relations between ...

  

Source: Crooks, Gavin E. - Department of Plant and Microbial Biology, University of California at Berkeley

 

Collection: Physics ; Mathematics ; Biotechnology

 
99 SCOP database in 2004: renements integrate structure and sequence family data
 

Summary:  and structural relationships. Protein domains in SCOP are hierarchically classi®ed into families, superfamilies... between protein domains and thus can lead to a rearrangement that uni®es distinct protein superfamilies... evolutionary origin. Currently these ...

  

Source: Brenner, Steven E. - Department of Plant and Microbial Biology, University of California at Berkeley

 

Collection: Biotechnology

 
100 ProteinProtein Docking Benchmark 2.0: An Update Julian Mintseris,1
 

Summary:  as the nonredundant unit. While the SCOP superfamily is commonly used as the cutoff point for protein structure... Protein­Protein Docking Benchmark 2.0: An Update Julian Mintseris,1 Kevin Wiehe,1 Brian Pierce,1... a new version of the Protein­Protein Docking Benchmark, reconstructed from the bottom up to ...

  

Source: Weng, Zhiping - Center for Advanced Genomic Technology, Boston University

 

Collection: Biotechnology


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