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Biochemical functional predictions for protein structures of unknown or uncertain function

Computational and structural biotechnology journal, 2015-01, Vol.13 (C), p.182-191

2015

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Probing remote residues important for catalysis in Escherichia coli ornithine transcarbamoylase

PloS one, 2020-02, Vol.15 (2), p.e0228487

2020

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Stereoselective Synthesis of β-Glycinamide Ribonucleotide

Molecules (Basel, Switzerland), 2022-04, Vol.27 (8), p.2528

2022

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Evaluating protein cross-linking as a therapeutic strategy to stabilize SOD1 variants in a mouse model of familial ALS

PLoS biology, 2024-01, Vol.22 (1), p.e3002462-e3002462

2024

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POOL server: machine learning application for functional site prediction in proteins

Bioinformatics, 2012-08, Vol.28 (15), p.2078-2079

2012

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THEMATICS: A Simple Computational Predictor of Enzyme Function from Structure

Proceedings of the National Academy of Sciences - PNAS, 2001-10, Vol.98 (22), p.12473-12478

2001

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Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D Structure and sequence properties

PLoS computational biology, 2009-01, Vol.5 (1), p.e1000266-e1000266

2009

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Identification and characterization of alternative sites and molecular probes for SARS-CoV-2 target proteins

Frontiers in chemistry, 2022-10, Vol.10, p.1017394-1017394

2022

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Identification of functional subclasses in the DJ-1 superfamily proteins

PLoS computational biology, 2007-01, Vol.3 (1), p.e10-e10

2007

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In Vitro and in Vivo Evaluation of 11C‑Labeled Azetidinecarboxylates for Imaging Monoacylglycerol Lipase by PET Imaging Studies

Journal of medicinal chemistry, 2018-03, Vol.61 (6), p.2278-2291

2018

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Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase from Pseudomonas putida

Biochemistry (Easton), 2011-06, Vol.50 (22), p.4923-4935

2011

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Selective prediction of interaction sites in protein structures with THEMATICS

BMC bioinformatics, 2007-04, Vol.8 (1), p.119-119, Article 119

2007

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Abstract 1151 Machine Learning for understanding enzyme function and effects of cancer-associated mutations

The Journal of biological chemistry, 2024-03, Vol.300 (3)

2024

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Enzyme active sites: Identification and prediction of function using computational chemistry

Current opinion in structural biology, 2022-06, Vol.74, p.102384-102384, Article 102384

2022

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Computed chemical properties for predicting protein function

Biophysical journal, 2022-02, Vol.121 (3), p.132a-132a

2022

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Prediction of active sites for protein structures from computed chemical properties

Bioinformatics, 2005-06, Vol.21 (suppl-1), p.i258-i265

2005

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Amino acid interactions that facilitate enzyme catalysis

The Journal of chemical physics, 2021-05, Vol.154 (19), p.195101-195101

2021

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Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity

Proteins, structure, function, and bioinformatics, 2011-07, Vol.79 (7), p.2146-2160

2011

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Machine learning for prediction of protein function and elucidation of enzyme function and control

Biophysical journal, 2024-02, Vol.123 (3), p.431a-431a

2024

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Analysis of electrostatic coupling throughout the laboratory evolution of a designed retroaldolase

Protein science, 2021-08, Vol.30 (8), p.1617-1627

2021

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Key interactions convert amino acid side chains into strong acids and bases in the active sites of enzymes

Biophysical journal, 2023-02, Vol.122 (3), p.462a-462a

2023

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Electrostatic fingerprints of catalytically active amino acids in enzymes

Protein science, 2022-05, Vol.31 (5), p.e4291-n/a

2022

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Functional annotation of haloacid dehalogenase superfamily structural genomics proteins

Biochemical journal, 2023-10, Vol.480 (19), p.1553-1569

2023

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Effects of Phosphorylation of ERK2 Kinase on the Properties of Active Site Amino Acids

The FASEB journal, 2022-05, Vol.36 (S1), p.n/a

2022

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Electrostatic Fingerprints of Catalytically Active Amino Acids in Enzymes

The FASEB journal, 2022-05, Vol.36 (S1), p.n/a

2022

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Biochemical functional predictions for protein structures of unknown or uncertain function

Probing remote residues important for catalysis in Escherichia coli ornithine transcarbamoylase

Stereoselective Synthesis of β-Glycinamide Ribonucleotide

Evaluating protein cross-linking as a therapeutic strategy to stabilize SOD1 variants in a mouse model of familial ALS

POOL server: machine learning application for functional site prediction in proteins

THEMATICS: A Simple Computational Predictor of Enzyme Function from Structure

Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D Structure and sequence properties

Identification and characterization of alternative sites and molecular probes for SARS-CoV-2 target proteins

Identification of functional subclasses in the DJ-1 superfamily proteins

In Vitro and in Vivo Evaluation of 11C‑Labeled Azetidinecarboxylates for Imaging Monoacylglycerol Lipase by PET Imaging Studies

Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase from Pseudomonas putida

Selective prediction of interaction sites in protein structures with THEMATICS

Abstract 1151 Machine Learning for understanding enzyme function and effects of cancer-associated mutations

Enzyme active sites: Identification and prediction of function using computational chemistry

Computed chemical properties for predicting protein function

Prediction of active sites for protein structures from computed chemical properties

Amino acid interactions that facilitate enzyme catalysis

Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity

Machine learning for prediction of protein function and elucidation of enzyme function and control

Analysis of electrostatic coupling throughout the laboratory evolution of a designed retroaldolase

Key interactions convert amino acid side chains into strong acids and bases in the active sites of enzymes

Electrostatic fingerprints of catalytically active amino acids in enzymes

Functional annotation of haloacid dehalogenase superfamily structural genomics proteins

Effects of Phosphorylation of ERK2 Kinase on the Properties of Active Site Amino Acids

Electrostatic Fingerprints of Catalytically Active Amino Acids in Enzymes

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