(Q28481310)

6

0 references

Marco De Vivo

object named as

Marco De Vivo

3

0 references

Alessio Lodola

object named as

Alessio Lodola

1

0 references

Marco Mor

object named as

Marco Mor

5

0 references

author name string

Davide Branduardi

2

0 references

Luigi Capoferri

4

0 references

Andrea Cavalli

Creative Commons CC0 License

7

0 references

language of work or name

English

0 references

publication date

2012

0 references

published in

PLOS One

0 references

volume

7

0 references

issue

2

0 references

page(s)

e32397

0 references

copyright license

start time

28 February 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

cites work

Structures of an isopenicillin N converting Ntn-hydrolase reveal different catalytic roles for the active site residues of precursor and mature enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Comparison of multiple Amber force fields and development of improved protein backbone parameters

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

The Amber biomolecular simulation programs

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Purification and characterization of recombinant, human acid ceramidase. Catalytic reactions and interactions with acid sphingomyelinase

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

The structure of the mammalian 20S proteasome at 2.75 A resolution

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Penicillin V acylase crystal structure reveals new Ntn-hydrolase family members

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

A protein catalytic framework with an N-terminal nucleophile is capable of self-activation

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Very fast empirical prediction and rationalization of protein pKa values

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Ab initio QM/MM free-energy studies of arginine deiminase catalysis: the protonation state of the Cys nucleophile

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Synthesis and structure-activity relationships of N-(2-oxo-3-oxetanyl)amides as N-acylethanolamine-hydrolyzing acid amidase inhibitors.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Selective N-acylethanolamine-hydrolyzing acid amidase inhibition reveals a key role for endogenous palmitoylethanolamide in inflammation.

29 September 2017

1 reference

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QM/MM methods for biomolecular systems

29 September 2017

1 reference

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Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome.

29 September 2017

1 reference

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Molecular targeting of acid ceramidase: implications to cancer therapy.

29 September 2017

1 reference

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Autoproteolytic cleavage and activation of human acid ceramidase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

The N-acylethanolamine-hydrolyzing acid amidase (NAAA).

29 September 2017

1 reference

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Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

29 September 2017

1 reference

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Crystal structure of the boronic acid-based proteasome inhibitor bortezomib in complex with the yeast 20S proteasome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Conjugated bile acid hydrolase is a tetrameric N-terminal thiol hydrolase with specific recognition of its cholyl but not of its tauryl product.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Molecular characterization of N-acylethanolamine-hydrolyzing acid amidase, a novel member of the choloylglycine hydrolase family with structural and functional similarity to acid ceramidase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Computer simulations of enzyme catalysis: methods, progress, and insights

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

The role of alpha-amino group of the N-terminal serine of beta subunit for enzyme catalysis and autoproteolytic activation of glutaryl 7-aminocephalosporanic acid acylase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Structural comparison of Ntn-hydrolases.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Purification and characterization of bile salt hydrolase from Clostridium perfringens

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Do N-terminal nucleophile hydrolases indeed have a single amino acid catalytic center?

2 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032397

A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032397

From A to B in free energy space.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032397

On the origin of the stabilization of the zwitterionic resting state of cysteine proteases: a theoretical study

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032397

What is so special about Arg 55 in the catalysis of cyclophilin A? insights from hybrid QM/MM simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032397

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032397

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032397

The implementation of a fast and accurate QM/MM potential method in Amber

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032397

Understanding the mechanism of deacylation reaction catalyzed by the serine carboxyl peptidase kumamolisin-As: insights from QM/MM free energy simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032397

Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032397

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032397

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032397

Structural and functional analysis of a conjugated bile salt hydrolase from Bifidobacterium longum reveals an evolutionary relationship with penicillin V acylase

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0032397

Methyl Phosphate Dianion Hydrolysis in Solution Characterized by Path Collective Variables Coupled with DFT-Based Enhanced Sampling Simulations

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3289653

Application of a SCC-DFTB QM/MM approach to the investigation of the catalytic mechanism of fatty acid amide hydrolase

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22389698

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Computational enzymology

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22389698