(Q36104862)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

title

Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1 (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

Claudio N. Cavasotto

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

author name string

Victor M Anisimov

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

Arturas Ziemys

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

Smitha Kizhake

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

Ziyan Yuan

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

publication date

16 November 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

Journal of Computer - Aided Molecular Design

16 January 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

volume

25

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

issue

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

page(s)

1071-1084

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1007/s10822-011-9484-3

16 January 2020

exact match

0 references

cites work

Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

All-atom empirical potential for molecular modeling and dynamics studies of proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Molecular basis of BACH1/FANCJ recognition by TopBP1 in DNA replication checkpoint control

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Protein flexibility and ligand recognition: challenges for molecular modeling

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Comparison of the structures and peptide binding specificities of the BRCT domains of MDC1 and BRCA1

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Structural characterization of BRCT-tetrapeptide binding interactions.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

CHARMM: the biomolecular simulation program

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Structural evidence for direct interactions between the BRCT domains of human BRCA1 and a phospho-peptide from human ACC1

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Phosphorylation of liver X receptor alpha selectively regulates target gene expression in macrophages

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

R.E.DD.B.: a database for RESP and ESP atomic charges, and force field libraries

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

The role of quantum mechanics in structure-based drug design

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

CCDC98 is a BRCA1-BRCT domain-binding protein involved in the DNA damage response

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Abraxas and RAP80 form a BRCA1 protein complex required for the DNA damage response

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Calculation of protein-ligand binding affinities.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Scalable molecular dynamics with NAMD

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Calculation of absolute protein-ligand binding free energy from computer simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

The role of BRCA1 in the cellular response to chemotherapy

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

DNA damage-induced cell cycle checkpoint control requires CtIP, a phosphorylation-dependent binding partner of BRCA1 C-terminal domains

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Empirical force fields for biological macromolecules: overview and issues.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Structural basis of BACH1 phosphopeptide recognition by BRCA1 tandem BRCT domains

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Structure of the BRCT Repeats of BRCA1 Bound to a BACH1 Phosphopeptide

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Recent advances in the development and application of implicit solvent models in biomolecule simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Force fields for protein simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

The BRCT Domain Is a Phospho-Protein Binding Domain

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

BRCT Repeats As Phosphopeptide-Binding Modules Involved in Protein Targeting

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

BACH1, a novel helicase-like protein, interacts directly with BRCA1 and contributes to its DNA repair function

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

VMD: visual molecular dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Monte Carlo-minimization approach to the multiple-minima problem in protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Free energy via molecular simulation: applications to chemical and biomolecular systems

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Structure-activity relationship studies to probe the phosphoprotein binding site on the carboxy terminal domains of the breast cancer susceptibility gene 1.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Empirically corrected DFT and semi-empirical methods for non-bonding interactions.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Importance of dispersion and electron correlation in ab initio protein folding

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

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

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

BRCA1 protein products ... Functional motifs...

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

23 Theoretical calculations of relative affinities of binding

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

Structural basis for cell cycle checkpoint control by the BRCA1-CtIP complex.

2 July 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

Is quantum mechanics necessary for predicting binding free energy?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

Assessing the role of polarization in docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

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/10.1007%2FS10822-011-9484-3

Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

Calculation of absolute protein-ligand binding affinity using path and endpoint approaches

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

Application of the PM6 method to modeling proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

Optimization of parameters for semiempirical methods I. Method

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

Hydration free energies using semiempirical quantum mechanical Hamiltonians and a continuum solvent model with multiple atomic-type parameters.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

Structure of the BRCT repeats of BRCA1 bound to a BACH1 phosphopeptide: implications for signaling

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3400539

A semiempirical model for the two-center repulsion integrals in the NDDO approximation

23 September 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-011-9484-3

Theory and applications of the generalized Born solvation model in macromolecular simulations

21 January 2018

1 reference

12 December 2020

Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules

1 reference

12 December 2020

Thermodynamics of phosphopeptide tethering to BRCT: the structural minima for inhibitor design

1 reference

12 December 2020

Calculation of protein-ligand interaction energies by a fragmentation approach combining high-level quantum chemistry with classical many-body effects

1 reference

12 December 2020

Androgen Receptor Mutations Identified in Prostate Cancer and Androgen Insensitivity Syndrome Display Aberrant ART-27 Coactivator Function

1 reference

12 December 2020

Scalaradial, a Dialdehyde-Containing Marine Metabolite That Causes an Unexpected Noncovalent PLA2 Inactivation

1 reference

12 December 2020

Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Mechanics

1 reference

12 December 2020

Quantum Mechanical Dynamics of Charge Transfer in Ubiquitin in Aqueous Solution

1 reference

12 December 2020

10.1007/S10822-011-9484-3

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

journals/jcamd/AnisimovZKYNC11

16 January 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22086652%20AND%20SRC:MED&resulttype=core&format=json

16 January 2020

PubMed publication ID

22086652

1 reference