Functional sites in protein families uncovered via an objective and automated graph theoretic approach (Q30164905)

9 June 2017

title

Functional sites in protein families uncovered via an objective and automated graph theoretic approach (English)

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9 June 2017

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Pramod P Wangikar

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9 June 2017

Ashish V Tendulkar

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9 June 2017

S Ramya

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9 June 2017

Deepali N Mali

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9 June 2017

Sunita Sarawagi

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9 June 2017

language of work or name

English

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publication date

1 February 2003

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Journal of Molecular Biology

9 June 2017

published in

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9 June 2017

volume

326

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9 June 2017

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9 June 2017

page(s)

955-978

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Structural genomics in North America.

9 June 2017

cites work

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Protein structure elucidation from NMR proton densities.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

De novo determination of protein structure by NMR using orientational and long-range order restraints

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Solution NMR structure of the myosin phosphatase inhibitor protein CPI-17 shows phosphorylation-induced conformational changes responsible for activation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Protein structure prediction constrained by solution X-ray scattering data and structural homology identification.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Threading with explicit models for evolutionary conservation of structure and sequence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Molecular dynamics in the endgame of protein structure prediction.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Use of structure comparison methods for the refinement of protein structure predictions. I. Identifying the structural family of a protein from low-resolution models.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Protein structure prediction and structural genomics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

7 January 2021

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The Protein Data Bank: a computer-based archival file for macromolecular structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Recent developments in computational proteomics.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Enhanced genome annotation using structural profiles in the program 3D-PSSM

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Prediction of functionally important residues based solely on the computed energetics of protein structure.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Sequence and structure-based prediction of eukaryotic protein phosphorylation sites

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

From genes to protein structure and function: novel applications of computational approaches in the genomic era.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Structural genomics programs at the US National Institute of General Medical Sciences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The classification and origins of protein folding patterns

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Protein structure comparison by alignment of distance matrices

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Assigning genomic sequences to CATH

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

SCOP: a structural classification of proteins database for the investigation of sequences and structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

SCOP: a structural classification of proteins database

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

New structure--novel fold?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Dictionary of recurrent domains in protein structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Touring protein fold space with Dali/FSSP

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The prediction and characterization of metal binding sites in proteins.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Automatic generation of primary sequence patterns from sets of related protein sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Identification of sequence motifs from a set of proteins with related function.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The PROSITE dictionary of sites and patterns in proteins, its current status

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The PROSITE database, its status in 1997.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

PRINTS-S: the database formerly known as PRINTS.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Superior performance in protein homology detection with the Blocks Database servers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Three-dimensional structure analysis of PROSITE patterns

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Structure of crystalline -chymotrypsin. II. A preliminary report including a hypothesis for the activation mechanism

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Dissecting the catalytic triad of a serine protease

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Catalytic triads and their relatives

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

A serine protease triad forms the catalytic centre of a triacylglycerol lipase

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Ser-His-Glu triad forms the catalytic site of the lipase from Geotrichum candidum

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Multicopper Oxidases and Oxygenases

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Genomic structure of the gene encoding the human GLI-related, Krüppel-like zinc finger protein GLIS2.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Details of the acyl-enzyme intermediate and the oxyanion hole in serine protease catalysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Unique fold and active site in cytomegalovirus protease

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Molecular markers of serine protease evolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Three-dimensional structure of guanylyl cyclase activating protein-2, a calcium-sensitive modulator of photoreceptor guanylyl cyclases

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Structure of Cdc4p, a contractile ring protein essential for cytokinesis in Schizosaccharomyces pombe

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The 2.2 A resolution structure of the O(H) blood-group-specific lectin I from Ulex europaeus

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Crystal structure of native and Cd/Cd-substituted Dioclea guianensis seed lectin. A novel manganese-binding site and structural basis of dimer-tetramer association

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The role of weak protein-protein interactions in multivalent lectin-carbohydrate binding: crystal structure of cross-linked FRIL

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The 2.15 A crystal structure of CG-16, the developmentally regulated homodimeric chicken galectin

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Structure and function of the Bacillus hybrid enzyme GluXyn-1: native-like jellyroll fold preserved after insertion of autonomous globular domain

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

1.8 A refined structure of the lipase from Geotrichum candidum

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Stereoselectivity of Mucorales lipases toward triradylglycerols--a simple solution to a complex problem

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Catalysis at the interface: the anatomy of a conformational change in a triglyceride lipase

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The structure of arylamine N-acetyltransferase from Mycobacterium smegmatis--an enzyme which inactivates the anti-tubercular drug, isoniazid

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 Å resolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Crystal structure of human osteoclast cathepsin K complex with E-64

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Contribution of the glutamine 19 side chain to transition-state stabilization in the oxyanion hole of papain

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Structure of arylamine N-acetyltransferase reveals a catalytic triad

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Conserved tryptophan in the core domain of transglutaminase is essential for catalytic activity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Two non-proline cis peptide bonds may be important for factor XIII function

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Crystal structure of red sea bream transglutaminase

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The three-dimensional structure of mammalian ribonucleotide reductase protein R2 reveals a more-accessible iron-radical site than Escherichia coli R2

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The high-resolution X-ray crystallographic structure of the ferritin (EcFtnA) of Escherichia coli; comparison with human H ferritin (HuHF) and the structures of the Fe(3+) and Zn(2+) derivatives

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1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Structure of the yeast ribonucleotide reductase Y2Y4 heterodimer

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The structure of chloroplast cytochrome c6 at 1.9 A resolution: evidence for functional oligomerization

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Crystal and molecular structure of barley alpha-amylase

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Crystal structures of amylosucrase from Neisseria polysaccharea in complex with D-glucose and the active site mutant Glu328Gln in complex with the natural substrate sucrose

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Subsite mapping of the human pancreatic alpha-amylase active site through structural, kinetic, and mutagenesis techniques

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Crystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

X-ray analyses of aspartic proteinases. IV. Structure and refinement at 2.2 A resolution of bovine chymosin

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

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7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

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7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

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7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Crystal structure of an acidic phospholipase A2 from the venom of Agkistrodon halys pallas at 2.0 A resolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

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7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

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7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

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7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

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7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

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7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

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7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

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7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The GLI gene encodes a nuclear protein which binds specific sequences in the human genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

GLI3 encodes a 190-kilodalton protein with multiple regions of GLI similarity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

A novel zinc finger protein, zic, is involved in neurogenesis, especially in the cell lineage of cerebellar granule cells

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Identification and characterization of Zic4, a new member of the mouse Zic gene family

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The expression of the mouse Zic1, Zic2, and Zic3 gene suggests an essential role for Zic genes in body pattern formation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Zinc Finger Domains: Hypotheses and Current Knowledge

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Lessons from zinc-binding peptides

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The three-dimensional structure of flavodoxin reductase from Escherichia coli at 1.7 A resolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

X-ray structure of the ferredoxin:NADP+ reductase from the cyanobacterium Anabaena PCC 7119 at 1.8 A resolution, and crystallographic studies of NADP+ binding at 2.25 A resolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Refined crystal structure of spinach ferredoxin reductase at 1.7 A resolution: oxidized, reduced and 2'-phospho-5'-AMP bound states

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

Structure of barley grain peroxidase refined at 1.9-A resolution. A plant peroxidase reversibly inactivated at neutral pH

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2901384-0

The crystal structure of lignin peroxidase at 1.70 A resolution reveals a hydroxy group on the cbeta of tryptophan 171: a novel radical site formed during the redox cycle

7 January 2021

1 reference

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10.1016/S0022-2836(02)01384-0

7 January 2021

Identifiers

DOI

1 reference

9 June 2017

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