(Q27902363)

David Sehnal

2

0 references

Radka Svobodová Vařeková

7

Radka Svobodová Vařeková

0 references

Crina-Maria Ionescu

1

Crina-Maria Ionescu

0 references

Stanislav Geidl

8

Stanislav Geidl

0 references

Tomáš Bouchal

6

Tomáš Bouchal

0 references

Jaroslav Koča

9

Jaroslav Koča

0 references

author name string

Francesco L Falginella

3

0 references

Purbaj Pant

Journal of Cheminformatics

4

0 references

publication date

2015

0 references

published in

1 reference

Creative Commons Attribution 4.0 International

volume

7

0 references

issue

1

0 references

page(s)

50

0 references

copyright license

start time

22 October 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

exact match

https://scigraph.springernature.com/pub.10.1186/s13321-015-0099-x

0 references

cites work

Cysteine deleted protegrin-1 (CDP-1): anti-bacterial activity, outer-membrane disruption and selectivity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Proteasome inhibitors block DNA repair and radiosensitize non-small cell lung cancer

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Finding MOFs for highly selective CO2/N2 adsorption using materials screening based on efficient assignment of atomic point charges

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Open Babel: An open chemical toolbox

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Solution structure of protegrin-1, a broad-spectrum antimicrobial peptide from porcine leukocytes

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Charge profile analysis reveals that activation of pro-apoptotic regulators Bax and Bak relies on charge transfer mediated allosteric regulation

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Automatic atom type and bond type perception in molecular mechanical calculations

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Improved Atoms-in-Molecule Charge Partitioning Functional for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic and Nonperiodic Materials

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

On the energy components governing molecular recognition in the framework of continuum approaches

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

DNA charge transport within the cell

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Antimicrobial potency and selectivity of simplified symmetric-end peptides

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

The modern pharmacology of paracetamol: therapeutic actions, mechanism of action, metabolism, toxicity and recent pharmacological findings

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Predicting pKa values from EEM atomic charges

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

The role of proteasome beta subunits in gastrin-mediated transcription of plasminogen activator inhibitor-2 and regenerating protein1

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

The pKa Cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Molecular dynamics simulations of three protegrin-type antimicrobial peptides: interplay between charges at the termini, β-sheet structure and amphiphilic interactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

The 26S proteasome: assembly and function of a destructive machine

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Assembly, structure, and function of the 26S 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=4613891

Electron transfer in peptides and proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Correlation between simulated physicochemical properties and hemolycity of protegrin-like antimicrobial peptides: predicting experimental toxicity.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Origin and control of superlinear polarizability scaling in chemical potential equalization methods

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Paracetamol: new vistas of an old drug

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Protegrin structure-activity relationships: using homology models of synthetic sequences to determine structural characteristics important for activity.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Design of non-cysteine-containing antimicrobial beta-hairpins: structure-activity relationship studies with linear protegrin-1 analogues

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Protegrins: new antibiotics of mammalian origin

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Protegrin-1: a broad-spectrum, rapidly microbicidal peptide with in vivo activity.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

QSAR study on the Ah receptor-binding affinities of polyhalogenated dibenzo-p-dioxins using net atomic-charge descriptors and a radial basis neural network

2 June 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

An Undulatory Theory of the Mechanics of Atoms and Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Electronic Structures of Molecules XI. Electroaffinity, Molecular Orbitals and Dipole Moments

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Natural population analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Bonded-atom fragments for describing molecular charge densities

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Accurate partial atomic charges for high-energy molecules using class IV charge models with the MIDI! basis set

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Toward an alternative hardness kernel matrix structure in the Electronegativity Equalization Method (EEM).

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

A modified electronegativity equalization method for fast and accurate calculation of atomic charges in large biological molecules.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Generating conformer ensembles using a multiobjective genetic algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Fast calculation of quantum chemical molecular descriptors from the electronegativity equalization method.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Assessment of Atomic Charge Models for Gas-Phase Computations on Polypeptides.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Electronegativity Equalization Method: Parameterization and Validation for Large Sets of Organic, Organohalogene and Organometal Molecule.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Predicting pK(a) values of substituted phenols from atomic charges: comparison of different quantum mechanical methods and charge distribution schemes

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Properties of atoms in molecules: Dipole moments and transferability of properties

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-015-0099-X

Rationalization of the pKa Values of Alcohols and Thiols Using Atomic Charge Descriptors and Its Application to the Prediction of Amino Acid pKa’s

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

The electronegativity equalization method and the split charge equilibration applied to organic systems: parametrization, validation, and comparison

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

Critical analysis and extension of the Hirshfeld atoms in molecules.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

A generalization of the charge equilibration method for nonmetallic materials

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4613891

A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26500704

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Chemically Meaningful Atomic Charges That Reproduce the Electrostatic Potential in Periodic and Nonperiodic Materials

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26500704

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26500704

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A chemical potential equalization method for molecular simulations

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1186/S13321-015-0099-X

A simple method for the fast calculation of charge redistribution of solutes in an implicit solvent model

2 January 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1186/S13321-015-0099-X

ITP Adjuster 1.0: A New Utility Program to Adjust Charges in the Topology Files Generated by the PRODRG Server

2 January 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1186/S13321-015-0099-X

Quantum-Mechanical Molecular Dynamics of Charge Transfer

2 January 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1186/S13321-015-0099-X

On the Non‐Orthogonality Problem Connected with the Use of Atomic Wave Functions in the Theory of Molecules and Crystals

2 January 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1186/S13321-015-0099-X

Extending and simplifying the electronegativity equalization method1Dedicated to Professor Herman van Bekkum on the occasion of his 65th birthday.1

2 January 2022

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1186/S13321-015-0099-X

cp2k: atomistic simulations of condensed matter systems

1 October 2023

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1186/S13321-015-0099-X

10.1186/S13321-015-0099-X

1 October 2023

Identifiers

DOI

0 references

DBLP publication ID

journals/jcheminf/IonescuSFPPBVGK15

1 reference

DBLP Dataset 2021-01-02