A protocol for CABS-dock protein-peptide docking driven by side-chain contact information. (Q41500458)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28830545 AND SRC:MED&resulttype=core&format=json

28 March 2020

title

A protocol for CABS-dock protein-peptide docking driven by side-chain contact information (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28830545 AND SRC:MED&resulttype=core&format=json

28 March 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28830545 AND SRC:MED&resulttype=core&format=json

28 March 2020

Andrzej Kolinski

4

0 references

Maciej Pawel Ciemny

series ordinal

3

object named as

Maciej Pawel Ciemny

1 reference

28 March 2020

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28830545 AND SRC:MED&resulttype=core&format=json

5

Sebastian Kmiecik

1 reference

28 March 2020

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28830545 AND SRC:MED&resulttype=core&format=json

Maciej Blaszczyk

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28830545 AND SRC:MED&resulttype=core&format=json

28 March 2020

publication date

18 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28830545 AND SRC:MED&resulttype=core&format=json

BioMedical Engineering OnLine

28 March 2020

published in

1 reference

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28 March 2020

volume

16

1 reference

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28 March 2020

issue

Suppl 1

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28 March 2020

page(s)

73

1 reference

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Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction.

28 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS Model

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Coarse-Grained Protein Models and Their Applications

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Comparative Protein Structure Modeling Using MODELLER.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Understanding the challenges of protein flexibility in drug design.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Peptide therapeutics: current status and future directions

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Sequence co-evolution gives 3D contacts and structures of protein complexes

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Structure prediction of the second extracellular loop in G-protein-coupled receptors

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

CABS-flex predictions of protein flexibility compared with NMR ensembles.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

CABS-fold: Server for the de novo and consensus-based prediction of protein structure

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

CABS-flex: Server for fast simulation of protein structure fluctuations

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

A unified conformational selection and induced fit approach to protein-peptide docking

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Rosetta FlexPepDock web server--high resolution modeling of peptide-protein interactions

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Analysis and optimization of interactions between peptides mimicking the GD2 ganglioside and the monoclonal antibody 14G2a

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions?

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acid

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Accurate prediction of peptide binding sites on protein surfaces.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Folding pathway of the b1 domain of protein G explored by multiscale modeling

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Characterization of protein-folding pathways by reduced-space modeling

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Protein modeling and structure prediction with a reduced representation.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Highly Flexible Protein-Peptide Docking Using CABS-Dock.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Mechanism of Folding and Binding of an Intrinsically Disordered Protein As Revealed by ab Initio Simulations.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Information-driven modeling of protein-peptide complexes

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Protein-peptide complex prediction through fragment interaction patterns

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Hierarchical modeling of protein interactions.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5568604

Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators' sequences

19 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28830545

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S12938-017-0363-6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28830545 AND SRC:MED&resulttype=core&format=json

Dimensions Publication ID

28 March 2020

0 references

1 reference

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28 March 2020

PubMed publication ID

28830545

1 reference