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Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions

Proteins, structure, function, and bioinformatics, 2005-10, Vol.61 (1), p.6-20

2005

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A method for simultaneous alignment of multiple protein structures

Proteins, structure, function, and bioinformatics, 2004-07, Vol.56 (1), p.143-156

2004

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The starch‐binding domain family CBM41—An in silico analysis of evolutionary relationships

Proteins, structure, function, and bioinformatics, 2017-08, Vol.85 (8), p.1480-1492

2017

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A study of a hierarchical structure of proteins and ligand binding sites of receptors using the triangular spatial relationship‐based structure comparison method and development of a size‐filtering feature designed for comparing different sizes of protein structures

Proteins, structure, function, and bioinformatics, 2022-01, Vol.90 (1), p.239-257

2022

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Ligand Binding Site Comparison — LiBiSCo — a web‐based tool for analyzing interactions between proteins and ligands to explore amino acid specificity within active sites

Proteins, structure, function, and bioinformatics, 2021-11, Vol.89 (11), p.1530-1540

2021

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G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

Protein science, 2016-04, Vol.25 (4), p.865-876

2016

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Structure-based classification of FAD binding sites: A comparative study of structural alignment tools

Proteins, structure, function, and bioinformatics, 2016-11, Vol.84 (11), p.1728-1747

2016

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Multiple diverse ligands binding at a single protein site: A matter of pre‐existing populations

Protein science, 2002-02, Vol.11 (2), p.184-197

2002

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Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison

Proteins, structure, function, and bioinformatics, 2012-04, Vol.80 (4), p.1177-1195

2012

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Structural Analysis of Xylose Isomerase from Streptomyces avermitilis

Crystals (Basel), 2024-05, Vol.14 (5), p.446

Nam, Ki Hyun

2024

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Structural and functional insight into the universal stress protein family

Evolutionary applications, 2013-04, Vol.6 (3), p.434-449

2013

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WW and SH3 domains, two different scaffolds to recognize proline-rich ligands

FEBS Letters, 2002-02, Vol.513 (1), p.30-37

2002

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Identification and Characterization of the Haloperoxidase VPO-RR from Rhodoplanes roseus by Genome Mining and Structure-Based Catalytic Site Mapping

Catalysts, 2022-10, Vol.12 (10), p.1195

2022

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Structural and Functional Studies of H. seropedicae RecA Protein - Insights into the Polymerization of RecA Protein as Nucleoprotein Filament

PloS one, 2016-07, Vol.11 (7), p.e0159871-e0159871

2016

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High‐resolution crystal structures of the photoreceptor glyceraldehyde 3‐phosphate dehydrogenase (GAPDH) with three and four‐bound NAD molecules

Protein science, 2014-11, Vol.23 (11), p.1629-1639

2014

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The specific applications of the TSR-based method in identifying Zn2+ binding sites of proteases and ACE/ACE2

Data in brief, 2022-12, Vol.45, p.108629-108629, Article 108629

2022

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Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon

Journal of molecular biology, 2007-09, Vol.372 (3), p.817-845

2007

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R Tutorial: Detection of Differentially Interacting Chromatin Regions From Multiple Hi‐C Datasets

Current Protocols in Bioinformatics, 2019-06, Vol.66 (1), p.e76-n/a

2019

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Crystal structure of juvenile hormone epoxide hydrolase from the silkworm Bombyx mori

Proteins, structure, function, and bioinformatics, 2014-11, Vol.82 (11), p.3224-3229

2014

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Fold Independent Structural Comparisons of Protein–Ligand Binding Sites for Exploring Functional Relationships

Journal of molecular biology, 2006-02, Vol.355 (5), p.1112-1124

2006

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Combining spatial and chemical information for clustering pharmacophores

BMC bioinformatics, 2014, Vol.15 Suppl 16 (Suppl 16), p.S5-S5, Article S5

2014

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Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: An automated all-against-all structural comparison using geometric matching

Proteins, structure, function, and bioinformatics, 2004-08, Vol.56 (2), p.250-260

2004

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GPU-Based Point Cloud Superpositioning for Structural Comparisons of Protein Binding Sites

IEEE/ACM transactions on computational biology and bioinformatics, 2018-05, Vol.15 (3), p.740-752

2018

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Structural Comparison and Simulation of Pneumococcal Peptidoglycan Hydrolase LytB

Methods in molecular biology (Clifton, N.J.), 2016, Vol.1440, p.271

2016

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Structural comparison of the active site channels in rodent and primate vascular adhesion protein-1

Journal of Neural Transmission, 2013-06, Vol.120 (6), p.947-950

2013

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Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions

A method for simultaneous alignment of multiple protein structures

The starch‐binding domain family CBM41—An in silico analysis of evolutionary relationships

A study of a hierarchical structure of proteins and ligand binding sites of receptors using the triangular spatial relationship‐based structure comparison method and development of a size‐filtering feature designed for comparing different sizes of protein structures

Ligand Binding Site Comparison — LiBiSCo — a web‐based tool for analyzing interactions between proteins and ligands to explore amino acid specificity within active sites

G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

Structure-based classification of FAD binding sites: A comparative study of structural alignment tools

Multiple diverse ligands binding at a single protein site: A matter of pre‐existing populations

Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison

Structural Analysis of Xylose Isomerase from Streptomyces avermitilis

Structural and functional insight into the universal stress protein family

WW and SH3 domains, two different scaffolds to recognize proline-rich ligands

Identification and Characterization of the Haloperoxidase VPO-RR from Rhodoplanes roseus by Genome Mining and Structure-Based Catalytic Site Mapping

Structural and Functional Studies of H. seropedicae RecA Protein - Insights into the Polymerization of RecA Protein as Nucleoprotein Filament

High‐resolution crystal structures of the photoreceptor glyceraldehyde 3‐phosphate dehydrogenase (GAPDH) with three and four‐bound NAD molecules

The specific applications of the TSR-based method in identifying Zn2+ binding sites of proteases and ACE/ACE2

Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon

R Tutorial: Detection of Differentially Interacting Chromatin Regions From Multiple Hi‐C Datasets

Crystal structure of juvenile hormone epoxide hydrolase from the silkworm Bombyx mori

Fold Independent Structural Comparisons of Protein–Ligand Binding Sites for Exploring Functional Relationships

Combining spatial and chemical information for clustering pharmacophores

Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: An automated all-against-all structural comparison using geometric matching

GPU-Based Point Cloud Superpositioning for Structural Comparisons of Protein Binding Sites

Structural Comparison and Simulation of Pneumococcal Peptidoglycan Hydrolase LytB

Structural comparison of the active site channels in rodent and primate vascular adhesion protein-1

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