Protein structure comparison by alignment of distance matrices.

PubWeight™: 34.74‹?› | Rank: Top 0.01% | All-Time Top 10000

🔗 View Article (PMID 8377180)

Published in J Mol Biol on September 05, 1993

Authors

L Holm1, C Sander

Author Affiliations

1: European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany.

Articles citing this

(truncated to the top 100)

TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15

Recent improvements to the PROSITE database. Nucleic Acids Res (2004) 11.89

Recognition of related proteins by iterative template refinement (ITR). Protein Sci (1994) 9.67

The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Res (1998) 9.59

LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res (2003) 9.44

Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J (2004) 8.19

Crystal structure of the extracellular segment of integrin alpha Vbeta3. Science (2001) 8.12

Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science (2010) 6.79

MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci (2002) 5.47

Integrating sequence and structural biology with DAS. BMC Bioinformatics (2007) 5.12

The FSSP database of structurally aligned protein fold families. Nucleic Acids Res (1994) 4.94

Crystal structure of the kinesin motor domain reveals a structural similarity to myosin. Nature (1996) 4.48

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J Mol Biol (2005) 4.02

An RNA cap (nucleoside-2'-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization. EMBO J (2002) 3.87

Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Proc Natl Acad Sci U S A (1999) 3.77

Can correct protein models be identified? Protein Sci (2003) 3.74

A unified statistical framework for sequence comparison and structure comparison. Proc Natl Acad Sci U S A (1998) 3.68

TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci (1997) 3.50

Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res (1997) 3.34

Structure of a flavin-binding plant photoreceptor domain: insights into light-mediated signal transduction. Proc Natl Acad Sci U S A (2001) 3.33

Structure and E3-ligase activity of the Ring-Ring complex of polycomb proteins Bmi1 and Ring1b. EMBO J (2006) 3.21

Directed evolution of a monomeric, bright and photostable version of Clavularia cyan fluorescent protein: structural characterization and applications in fluorescence imaging. Biochem J (2006) 3.20

The crystal structure of the quorum sensing protein TraR bound to its autoinducer and target DNA. EMBO J (2002) 3.11

Three-dimensional structures of membrane proteins from genomic sequencing. Cell (2012) 3.02

Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes. Genome Biol (2003) 3.02

High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry. Proc Natl Acad Sci U S A (2000) 2.96

Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease. Nature (2006) 2.95

Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2. EMBO J (2003) 2.95

Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci U S A (2002) 2.92

Flexibility in DNA recombination: structure of the lambda integrase catalytic core. Science (1997) 2.91

F-actin-like filaments formed by plasmid segregation protein ParM. EMBO J (2002) 2.91

Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE). J Biol Chem (2011) 2.86

Crystal structure of the BTB domain from PLZF. Proc Natl Acad Sci U S A (1998) 2.84

Placement of the structural proteins in Sindbis virus. J Virol (2002) 2.81

A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator. Proc Natl Acad Sci U S A (1998) 2.77

New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol (2003) 2.77

Position of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing. Genes Dev (2003) 2.77

The Protein Model Portal--a comprehensive resource for protein structure and model information. Database (Oxford) (2013) 2.76

Crystal structure of a bacterial family-III cellulose-binding domain: a general mechanism for attachment to cellulose. EMBO J (1996) 2.74

Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. Proc Natl Acad Sci U S A (1998) 2.70

Structure of an XRCC1 BRCT domain: a new protein-protein interaction module. EMBO J (1998) 2.68

High-resolution structure of the E.coli RecQ helicase catalytic core. EMBO J (2003) 2.61

Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins. Protein Sci (1998) 2.60

Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. PLoS Pathog (2008) 2.60

JAMM: a metalloprotease-like zinc site in the proteasome and signalosome. PLoS Biol (2003) 2.56

Structural and functional similarities between the capsid proteins of bacteriophages T4 and HK97 point to a common ancestry. Proc Natl Acad Sci U S A (2005) 2.53

BluB cannibalizes flavin to form the lower ligand of vitamin B12. Nature (2007) 2.53

The structural alignment between two proteins: is there a unique answer? Protein Sci (1996) 2.50

Structural basis of the membrane-targeting and unmasking mechanisms of the radixin FERM domain. EMBO J (2000) 2.49

FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res (2004) 2.49

Ligand-induced asymmetry in histidine sensor kinase complex regulates quorum sensing. Cell (2006) 2.48

The structure of the mRNA export factor TAP reveals a cis arrangement of a non-canonical RNP domain and an LRR domain. EMBO J (2000) 2.44

The HSSP database of protein structure-sequence alignments. Nucleic Acids Res (1997) 2.44

Structure of Thermotoga maritima stationary phase survival protein SurE: a novel acid phosphatase. Structure (2001) 2.43

Crystal structure of an oxygen-binding heme domain related to soluble guanylate cyclases. Proc Natl Acad Sci U S A (2004) 2.41

The rhesus rotavirus VP4 sialic acid binding domain has a galectin fold with a novel carbohydrate binding site. EMBO J (2002) 2.41

The structural basis of cyclic diguanylate signal transduction by PilZ domains. EMBO J (2007) 2.39

Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci (2006) 2.39

Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase. Proc Natl Acad Sci U S A (2008) 2.36

Emergence of protein fold families through rational design. PLoS Comput Biol (2006) 2.35

Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain. EMBO J (2002) 2.30

MATRAS: A program for protein 3D structure comparison. Nucleic Acids Res (2003) 2.29

Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution. EMBO J (1997) 2.29

Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics (2010) 2.28

Structure of the reovirus membrane-penetration protein, Mu1, in a complex with is protector protein, Sigma3. Cell (2002) 2.24

The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat Struct Biol (2002) 2.24

Structure and interactions of the translation initiation factor eIF1. EMBO J (1999) 2.24

KH domain: one motif, two folds. Nucleic Acids Res (2001) 2.21

Protein function annotation by homology-based inference. Genome Biol (2009) 2.20

ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification. BMC Bioinformatics (2006) 2.18

Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. EMBO J (2006) 2.16

The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll. EMBO J (2004) 2.15

RNA-specific ribonucleotidyl transferases. RNA (2007) 2.15

Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res (2003) 2.14

The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res (1996) 2.10

Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain. Proc Natl Acad Sci U S A (1998) 2.10

Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition. EMBO J (2002) 2.09

Crystal structure of the matrix protein VP40 from Ebola virus. EMBO J (2000) 2.08

Crystal structure of a Baeyer-Villiger monooxygenase. Proc Natl Acad Sci U S A (2004) 2.07

CORA--topological fingerprints for protein structural families. Protein Sci (1999) 2.06

A novel variant of the immunoglobulin fold in surface adhesins of Staphylococcus aureus: crystal structure of the fibrinogen-binding MSCRAMM, clumping factor A. EMBO J (2002) 2.06

Crystal structure of reovirus attachment protein sigma1 reveals evolutionary relationship to adenovirus fiber. EMBO J (2002) 2.06

Crystal structure of MalK, the ATPase subunit of the trehalose/maltose ABC transporter of the archaeon Thermococcus litoralis. EMBO J (2000) 2.05

Automatic classification of protein structure by using Gauss integrals. Proc Natl Acad Sci U S A (2002) 2.03

Local feature frequency profile: a method to measure structural similarity in proteins. Proc Natl Acad Sci U S A (2004) 2.03

DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA. EMBO J (2000) 2.01

Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging. PLoS Biol (2006) 1.99

AlgK is a TPR-containing protein and the periplasmic component of a novel exopolysaccharide secretin. Structure (2010) 1.97

Crystal structure of the cell division protein FtsA from Thermotoga maritima. EMBO J (2000) 1.97

Structure of the Dengue virus helicase/nucleoside triphosphatase catalytic domain at a resolution of 2.4 A. J Virol (2005) 1.96

Crystal structure at 2.6-A resolution of human macrophage migration inhibitory factor. Proc Natl Acad Sci U S A (1996) 1.95

An NMR approach to structural proteomics. Proc Natl Acad Sci U S A (2002) 1.95

Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3). J Biol Chem (2011) 1.94

IgG4 breaking the rules. Immunology (2002) 1.93

Structural genomics: a pipeline for providing structures for the biologist. Protein Sci (2002) 1.91

A novel evolutionarily conserved domain of cell-adhesion GPCRs mediates autoproteolysis. EMBO J (2012) 1.91

The crystal structure and mechanism of orotidine 5'-monophosphate decarboxylase. Proc Natl Acad Sci U S A (2000) 1.90

CD81 extracellular domain 3D structure: insight into the tetraspanin superfamily structural motifs. EMBO J (2001) 1.90

Structural changes of bacteriophage phi29 upon DNA packaging and release. EMBO J (2006) 1.90

TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences. BMC Bioinformatics (2007) 1.89

Articles by these authors

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69

Errors in protein structures. Nature (1996) 18.70

Touring protein fold space with Dali/FSSP. Nucleic Acids Res (1998) 18.00

Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol (1993) 17.53

Selection of representative protein data sets. Protein Sci (1992) 15.62

Dali: a network tool for protein structure comparison. Trends Biochem Sci (1995) 14.13

Automated genome sequence analysis and annotation. Bioinformatics (1999) 13.92

Mapping the protein universe. Science (1996) 13.72

Combining evolutionary information and neural networks to predict protein secondary structure. Proteins (1994) 9.97

The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Res (1998) 9.59

New structure--novel fold? Structure (1997) 9.19

Enlarged representative set of protein structures. Protein Sci (1994) 7.98

PHD--an automatic mail server for protein secondary structure prediction. Comput Appl Biosci (1994) 6.71

An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc Natl Acad Sci U S A (1992) 6.18

Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins (1996) 5.83

Completeness in structural genomics. Nat Struct Biol (2001) 5.36

Correlated mutations and residue contacts in proteins. Proteins (1994) 5.20

A yeast gene encoding a protein homologous to the human c-has/bas proto-oncogene product. Nature (1984) 5.19

Transmembrane helices predicted at 95% accuracy. Protein Sci (1995) 5.05

The FSSP database of structurally aligned protein fold families. Nucleic Acids Res (1994) 4.94

A database of protein structure families with common folding motifs. Protein Sci (1992) 4.77

The primary structure of transcription factor TFIIIA has 12 consecutive repeats. FEBS Lett (1985) 4.73

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol (1985) 4.56

MView: a web-compatible database search or multiple alignment viewer. Bioinformatics (1998) 4.50

The immunoglobulin fold. Structural classification, sequence patterns and common core. J Mol Biol (1994) 4.43

An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins (1997) 4.42

Conservation and prediction of solvent accessibility in protein families. Proteins (1994) 4.29

An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors. Oncogene (2009) 4.10

On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc Natl Acad Sci U S A (1984) 4.08

Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc Natl Acad Sci U S A (1993) 3.92

Searching protein structure databases has come of age. Proteins (1994) 3.87

Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors. J Mol Biol (1991) 3.81

Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics (1998) 3.47

Bioinformatics: from genome data to biological knowledge. Curr Opin Biotechnol (1997) 3.44

Dictionary of recurrent domains in protein structures. Proteins (1998) 3.40

Protein folds and families: sequence and structure alignments. Nucleic Acids Res (1999) 3.38

The ras protein family: evolutionary tree and role of conserved amino acids. Biochemistry (1991) 3.38

Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res (1997) 3.34

A method to predict functional residues in proteins. Nat Struct Biol (1995) 3.33

Parser for protein folding units. Proteins (1994) 3.25

Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases. Protein Sci (1993) 3.25

A sequence property approach to searching protein databases. J Mol Biol (1995) 2.86

Yeast chromosome III: new gene functions. EMBO J (1994) 2.85

Fast and simple Monte Carlo algorithm for side chain optimization in proteins: application to model building by homology. Proteins (1992) 2.69

Dipoles of the alpha-helix and beta-sheet: their role in protein folding. Nature (1981) 2.56

Detection of common three-dimensional substructures in proteins. Proteins (1991) 2.53

Evaluation of protein models by atomic solvation preference. J Mol Biol (1992) 2.53

Protein fold recognition by prediction-based threading. J Mol Biol (1997) 2.51

Molecular cloning of YPT1/SEC4-related cDNAs from an epithelial cell line. Mol Cell Biol (1990) 2.51

CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts. Bioinformatics (2000) 2.50

The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. Comput Appl Biosci (1996) 2.46

The HSSP database of protein structure-sequence alignments. Nucleic Acids Res (1997) 2.44

DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily. Trends Biochem Sci (1995) 2.41

A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme? Nucleic Acids Res (1994) 2.37

Progress in protein structure prediction? Trends Biochem Sci (1993) 2.34

Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng (1994) 2.30

Predicting protein structure using hidden Markov models. Proteins (1997) 2.20

The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res (1996) 2.10

How good are predictions of protein secondary structure? FEBS Lett (1983) 2.08

The GeneQuiz web server: protein functional analysis through the Web. Trends Biochem Sci (2000) 2.07

The ten helical twist angles of B-DNA. Nucleic Acids Res (1982) 2.02

Correlation between the structure and biochemical activities of FtsA, an essential cell division protein of the actin family. EMBO J (1994) 2.01

Genome sequences and great expectations. Genome Biol (2000) 1.98

TFIIB, an evolutionary link between the transcription machineries of archaebacteria and eukaryotes. Cell (1992) 1.91

Redefining the goals of protein secondary structure prediction. J Mol Biol (1994) 1.84

Decision support system for the evolutionary classification of protein structures. Proc Int Conf Intell Syst Mol Biol (1997) 1.80

Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology. Mol Microbiol (1995) 1.74

Enzyme HIT. Trends Biochem Sci (1997) 1.74

The essential tyrosine of the internalization signal in lysosomal acid phosphatase is part of a beta turn. Cell (1991) 1.72

The chaperone function of DnaK requires the coupling of ATPase activity with substrate binding through residue E171. EMBO J (1994) 1.71

The HSSP database of protein structure-sequence alignments. Nucleic Acids Res (1996) 1.70

Homology of the NifS family of proteins to a new class of pyridoxal phosphate-dependent enzymes. FEBS Lett (1993) 1.69

A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor. FEBS Lett (1992) 1.69

Transverse-momentum and pseudorapidity distributions of charged hadrons in pp collisions at square root of s = 7 TeV. Phys Rev Lett (2010) 1.67

Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III. Protein Sci (1992) 1.64

Challenging times for bioinformatics. Nature (1995) 1.63

A module of the DnaJ heat shock proteins found in malaria parasites. Trends Biochem Sci (1992) 1.60

Three sisters, different names. Nat Struct Biol (1994) 1.58

Study of the mass and spin-parity of the Higgs boson candidate via its decays to Z boson pairs. Phys Rev Lett (2013) 1.56

Objectively judging the quality of a protein structure from a Ramachandran plot. Comput Appl Biosci (1997) 1.52

Polarity as a criterion in protein design. Protein Eng (1989) 1.50

EUCLID: automatic classification of proteins in functional classes by their database annotations. Bioinformatics (1998) 1.49

Jury returns on structure prediction. Nature (1992) 1.48

Alignment of three-dimensional protein structures: network server for database searching. Methods Enzymol (1996) 1.45

A new ATP-binding fold in actin, hexokinase and Hsc70. Trends Cell Biol (1993) 1.44

New triple-helical model for the shaft of the adenovirus fibre. J Mol Biol (1992) 1.42

Computational comparisons of model genomes. Trends Biotechnol (1996) 1.38

Molecular cloning and structural analysis of genes from Zea mays (L.) coding for members of the ras-related ypt gene family. Proc Natl Acad Sci U S A (1992) 1.35

The use of position-specific rotamers in model building by homology. Proteins (1995) 1.35

Immunization with synthetic peptides of a Plasmodium falciparum surface antigen induces antimerozoite antibodies. Proc Natl Acad Sci U S A (1986) 1.32

Excluded volume approximation to protein-solvent interaction. The solvent contact model. Biophys J (1990) 1.30

Molecular modelling of the Norrie disease protein predicts a cystine knot growth factor tertiary structure. Nat Genet (1993) 1.25

Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. J Mol Biol (1993) 1.25

Antiparallel and parallel beta-strands differ in amino acid residue preferences. Nature (1979) 1.24

What's in a genome? Nature (1992) 1.24

Measurement of the electron charge asymmetry in inclusive W production in pp collisions at sqrt[s]=7  TeV. Phys Rev Lett (2012) 1.23

Specific recognition in the tertiary structure of beta-sheets of proteins. J Mol Biol (1980) 1.22

Progress of 1D protein structure prediction at last. Proteins (1995) 1.20

A hybrid protein kinase-RNase in an interferon-induced pathway? FEBS Lett (1993) 1.20