(Q33900072)

29 July 2017

title

Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors (English)

1 reference

29 July 2017

4

Ora Schueler-Furman

0 references

author name string

Barak Raveh

series ordinal

1

1 reference

29 July 2017

Nir London

series ordinal

2

1 reference

29 July 2017

Lior Zimmerman

series ordinal

3

1 reference

29 July 2017

language of work or name

English

0 references

publication date

29 April 2011

1 reference

29 July 2017

1 reference

29 July 2017

volume

6

1 reference

29 July 2017

issue

4

1 reference

29 July 2017

page(s)

e18934

1 reference

Creative Commons Attribution 4.0 International

29 July 2017

copyright license

start time

29 April 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Computational design of peptide ligands

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Peptide phage display as a tool for drug discovery: targeting membrane receptors

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Autophosphorylation Activates Dictyostelium Myosin II Heavy Chain Kinase A by Providing a Ligand for an Allosteric Binding Site in the -Kinase Domain

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

High-resolution mapping of protein sequence-function relationships

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Determinants of BH3 Binding Specificity for Mcl-1 versus Bcl-xL

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

The structural basis of peptide-protein binding strategies.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

The synergistic use of computation, chemistry and biology to discover novel peptide-based drugs: the time is right

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Synthetic therapeutic peptides: science and market

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Peptidic modulators of protein-protein interactions: progress and challenges in computational design

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Linking folding and binding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Approved drug mimics of short peptide ligands from protein interaction motifs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Contextual specificity in peptide-mediated protein interactions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Macromolecular modeling with rosetta

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Peptide ligand screening of alpha-synuclein aggregation modulators by in silico panning

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Yeast surface display for protein engineering and characterization

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Characterization of molecular recognition features, MoRFs, and their binding partners

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Paxillin and ponsin interact in nascent costameres of muscle cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin Omp32.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Systematic discovery of new recognition peptides mediating protein interaction networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Improved side-chain modeling for protein-protein docking

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Phage display-derived peptides as therapeutic alternatives to antibodies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Protein structure prediction using Rosetta

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Assembly of Cell Regulatory Systems Through Protein Interaction Domains

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Efficient docking of peptides to proteins without prior knowledge of the binding site

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Combinatorial alanine-scanning

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Angiotensin II type 1 receptor blockers

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Phage display for selection of novel binding peptides

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Native protein sequences are close to optimal for their structures

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

28 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Protein secondary structure prediction based on position-specific scoring matrices

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Identification of protein-protein interfaces by decreased amide proton solvent accessibility

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Bayesian statistical analysis of protein side-chain rotamer preferences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis.

28 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018934

PepX: a structural database of non-redundant protein-peptide complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018934

Protein-peptide interactions adopt the same structural motifs as monomeric protein folds

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018934

Studying protein-protein interactions using peptide arrays.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018934

Allosteric regulation of glycogen synthase kinase 3β: a theoretical study

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018934

DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018934

A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018934

Accurate prediction of peptide binding sites on protein surfaces.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018934

Knowledge-based protein secondary structure assignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018934

Atypical polyproline recognition by the CMS N-terminal Src homology 3 domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018934

Crystal structure of GRIP1 PDZ6-peptide complex reveals the structural basis for class II PDZ target recognition and PDZ domain-mediated multimerization

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018934

Crystal structures of beryllium fluoride-free and beryllium fluoride-bound CheY in complex with the conserved C-terminal peptide of CheZ reveal dual binding modes specific to CheY conformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018934

Peptide-mediated interactions in biological systems: new discoveries and applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018934

The Escherichia coli extracellular death factor EDF induces the endoribonucleolytic activities of the toxins MazF and ChpBK.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Sub-angstrom modeling of complexes between flexible peptides and globular proteins.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

Chemical structures and mode of action of intravenous glycoprotein IIb/IIIa receptor blockers: A review

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3084719

A Flexible Docking Procedure for the Exploration of Peptide Binding Selectivity to Known Structures and Homology Models of PDZ Domains

29 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21572516

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Crystallographic identification and functional characterization of phospholipids as ligands for the orphan nuclear receptor steroidogenic factor-1

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21572516

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0018934

1 reference

29 July 2017

0 references

1 reference

29 July 2017

1 reference