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Landscape of protein–small ligand binding modes

Protein science, 2016-09, Vol.25 (9), p.1659-1671

2016

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Ligand-binding site prediction of proteins based on known fragment–fragment interactions

Bioinformatics, 2010-06, Vol.26 (12), p.1493-1499

2010

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Identification of Dominant Transcripts in Oxidative Stress Response by a Full-Length Transcriptome Analysis

Molecular and cellular biology, 2021-02, Vol.41 (2)

2021

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Identification of protein functions from a molecular surface database, eF-site

Journal of structural and functional genomics, 2002, Vol.2 (1), p.9-22

2002

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Identification of protein biochemical functions by similarity search using the molecular surface database eF‐site

Protein science, 2003-08, Vol.12 (8), p.1589-1595

2003

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Ion concentration-dependent ion conduction mechanism of a voltage-sensitive potassium channel

PloS one, 2013-02, Vol.8 (2), p.e56342-e56342

2013

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eF-site and PDBjViewer: database and viewer for protein functional sites

Bioinformatics, 2004-05, Vol.20 (8), p.1329-1330

2004

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Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information

Proteins, structure, function, and bioinformatics, 2007-02, Vol.66 (3), p.655-663

2007

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Dynamic features of homodimer interfaces calculated by normal‐mode analysis

Protein science, 2012-10, Vol.21 (10), p.1503-1513

2012

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Structure-based prediction of DNA-binding sites on proteins Using the empirical preference of electrostatic potential and the shape of molecular surfaces

Proteins, structure, function, and bioinformatics, 2004-06, Vol.55 (4), p.885-894

2004

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Development of new indices to evaluate protein–protein interfaces: Assembling space volume, assembling space distance, and global shape descriptor

Journal of molecular graphics & modelling, 2009-02, Vol.27 (6), p.706-711

2009

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Prediction of Catalytic Residues in Enzymes Based on Known Tertiary Structure, Stability Profile, and Sequence Conservation

Journal of molecular biology, 2003-04, Vol.327 (5), p.1053-1064

2003

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Distribution of single‐nucleotide variants on protein–protein interaction sites and its relationship with minor allele frequency

Protein science, 2016-02, Vol.25 (2), p.316-321

2016

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Similarities and differences in the structure and function of 4.1G and 4.1R135, two protein 4.1 paralogues expressed in erythroid cells

Biochemical journal, 2010-12, Vol.432 (2), p.407-416

2010

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Identification of transient hub proteins and the possible structural basis for their multiple interactions

Protein science, 2008-01, Vol.17 (1), p.72-78

2008

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Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein–mononucleotide complexes

Protein engineering, 1999-01, Vol.12 (1), p.11-14

1999

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Probabilistic description of protein alignments for sequences and structures

Proteins, structure, function, and bioinformatics, 2004-07, Vol.56 (1), p.157-166

2004

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Mutational Analysis of Block and Facilitation of HERG Current by A Class III Anti-Arrhythmic Agent, Nifekalant

Channels (Austin, Tex.), 2007-05, Vol.1 (3), p.198-208

2007

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Finding evolutionary relations beyond superfamilies: Fold‐based superfamilies

Protein science, 2003-10, Vol.12 (10), p.2239-2251

2003

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Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8

Protein science, 2003-08, Vol.12 (8), p.1621-1632

2003

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Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states

Proteins, structure, function, and bioinformatics, 2011-05, Vol.79 (5), p.1550-1563

2011

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Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity

Protein engineering, design and selection, 2006-09, Vol.19 (9), p.421-429

2006

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Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

Journal of molecular biology, 2011-11, Vol.414 (2), p.289-302

2011

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eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape

Nucleic acids research, 2007-07, Vol.35 (Web Server issue), p.W398

2007

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Blind prediction of interfacial water positions in CAPRI

Proteins, structure, function, and bioinformatics, 2014-04, Vol.82 (4), p.620-632

2014

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Landscape of protein–small ligand binding modes

Ligand-binding site prediction of proteins based on known fragment–fragment interactions

Identification of Dominant Transcripts in Oxidative Stress Response by a Full-Length Transcriptome Analysis

Identification of protein functions from a molecular surface database, eF-site

Identification of protein biochemical functions by similarity search using the molecular surface database eF‐site

Ion concentration-dependent ion conduction mechanism of a voltage-sensitive potassium channel

eF-site and PDBjViewer: database and viewer for protein functional sites

Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information

Dynamic features of homodimer interfaces calculated by normal‐mode analysis

Structure-based prediction of DNA-binding sites on proteins Using the empirical preference of electrostatic potential and the shape of molecular surfaces

Development of new indices to evaluate protein–protein interfaces: Assembling space volume, assembling space distance, and global shape descriptor

Prediction of Catalytic Residues in Enzymes Based on Known Tertiary Structure, Stability Profile, and Sequence Conservation

Distribution of single‐nucleotide variants on protein–protein interaction sites and its relationship with minor allele frequency

Similarities and differences in the structure and function of 4.1G and 4.1R135, two protein 4.1 paralogues expressed in erythroid cells

Identification of transient hub proteins and the possible structural basis for their multiple interactions

Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein–mononucleotide complexes

Probabilistic description of protein alignments for sequences and structures

Mutational Analysis of Block and Facilitation of HERG Current by A Class III Anti-Arrhythmic Agent, Nifekalant

Finding evolutionary relations beyond superfamilies: Fold‐based superfamilies

Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8

Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states

Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape

Blind prediction of interfacial water positions in CAPRI

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