(Q34578072)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21339984%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

title

Computational docking of antibody-antigen complexes, opportunities and pitfalls illustrated by influenza hemagglutinin (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21339984%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

1 reference

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21339984%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

Luca Varani

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21339984%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

author name string

Mattia Pedotti

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21339984%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

Elsa Livoti

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21339984%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

language of work or name

English

0 references

publication date

5 January 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21339984%20AND%20SRC:MED&resulttype=core&format=json

International Journal of Molecular Sciences

23 January 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21339984%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

volume

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21339984%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21339984%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

page(s)

226-251

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21339984%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

23 January 2020

copyright license

start time

5 January 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

SwarmDock and the use of normal modes in protein-protein docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

The HADDOCK web server for data-driven biomolecular docking

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

I-TASSER: a unified platform for automated protein structure and function prediction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Rapid structural characterization of human antibody-antigen complexes through experimentally validated computational docking

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

RosettaAntibody: antibody variable region homology modeling server

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Seasonal influenza vaccines: evolutions and future trends

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Antibody recognition of a highly conserved influenza virus epitope

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Structural assembly of two-domain proteins by rigid-body docking

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

PIGS: automatic prediction of antibody structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

The RosettaDock server for local protein-protein docking

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Antibody-protein interactions: benchmark datasets and prediction tools evaluation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Assessing the energy landscape of CAPRI targets by FunHunt

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

RosettaDock in CAPRI rounds 6-12

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Improved side-chain modeling for protein-protein docking

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Structural differences among antibodies of different specificities

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Studies on structural units of the gamma-globulins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Protein-protein docking predictions for the CAPRI experiment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

CAPRI: a Critical Assessment of PRedicted Interactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Cyclic coordinate descent: A robotics algorithm for protein loop closure.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

HADDOCK: a protein-protein docking approach based on biochemical or biophysical information

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Principles of docking: An overview of search algorithms and a guide to scoring functions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

WAM: an improved algorithm for modelling antibodies on the WEB.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear overhauser enhancement data and dipolar couplings by rigid body minimization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Antibody modeling: implications for engineering and design.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Effective energy function for proteins in solution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Standard conformations for the canonical structures of immunoglobulins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Bayesian statistical analysis of protein side-chain rotamer preferences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Immunization with purified N1 and N2 influenza virus neuraminidases demonstrates cross-reactivity without antigenic competition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Domain association in immunoglobulin molecules. The packing of variable domains

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Using known substructures in protein model building and crystallography

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Structure of antibody hypervariable loops reproduced by a conformational search algorithm

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Analysis of genetic variability and mapping of point mutations in influenza virus by the RNase A mismatch cleavage method

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

An algorithm for determining the conformation of polypeptide segments in proteins by systematic search

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

The variability of genes of influenza A (H3N2) virus strains isolated in the G.D.R. during the 1970-1978 epidemic seasons.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Conformations of immunoglobulin hypervariable regions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Antibody-antigen complexes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Modelling of the combining sites of three anti-lysozyme monoclonal antibodies and of the complex between one of the antibodies and its epitope

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Basic local alignment search tool

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Framework residue 71 is a major determinant of the position and conformation of the second hypervariable region in the VH domains of immunoglobulins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Structural evidence for induced fit as a mechanism for antibody-antigen recognition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Antibody structure, prediction and redesign

7 July 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

Conformations of the third hypervariable region in the VH domain of immunoglobulins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

Scoring docked conformations generated by rigid-body protein-protein docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

Improving CAPRI predictions: optimized desolvation for rigid-body docking

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

Effect of local shape modifications of molecular surfaces on rigid-body protein–protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

Orientational sampling and rigid-body minimization in molecular docking

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

Rigid-body docking with mutant constraints of influenza hemagglutinin with antibody HC19.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

Probing fragment complementation by rigid-body docking: in silico reconstitution of calbindin D9k.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

Prediction of MEF2A-DNA interface by rigid body docking: a tool for fast estimation of protein mutational effects on DNA binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

ZDOCK: an initial-stage protein-docking algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

Protein-protein docking with backbone flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

FunHunt: model selection based on energy landscape characteristics.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3039950

Principles of docking: An overview of search algorithms and a guide to scoring functions

27 October 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS12010226

Prediction of the folding of short polypeptide segments by uniform conformational sampling

21 January 2018

1 reference

12 December 2020

Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition

1 reference

12 December 2020

Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations

1 reference

12 December 2020

ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5

1 reference

12 December 2020

The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure

1 reference

12 December 2020

Possible three-dimensional backbone folding around antibody combining site of immunoglobulin MOPC167

1 reference

12 December 2020

[Peptide mapping of the monoclonal antibodies against the heavy chain hemagglutinin from influenza virus H3N2]

1 reference

12 December 2020

The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking

1 reference

12 December 2020

A predictive method for determining possible three-dimensional foldings of immunoglobulin backbones around antibody combining sites

1 reference

12 December 2020

Canonical structures for the hypervariable regions of immunoglobulins

1 reference

12 December 2020

Structural classification of CDR-H3 in antibodies

1 reference

12 December 2020

[Variability of hemagglutinin from strains of influenza virus A (H3N2), isolated in Russian from 1989 to 1999]

1 reference

12 December 2020

Allosteric effects of a monoclonal antibody against thrombin exosite II

1 reference

12 December 2020

Identifiers

DOI

10.3390/IJMS12010226

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21339984%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21339984%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

PubMed publication ID

21339984

1 reference