Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization. (Q39251813)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24519881%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

title

Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization (English)

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7 March 2020

1

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7 March 2020

Daisuke Kuroda

2

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7 March 2020

author name string

Nicholas Marze

3

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7 March 2020

Jianqing Xu

4

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7 March 2020

Jeffrey J Gray

5

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7 March 2020

language of work or name

English

0 references

publication date

31 March 2014

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7 March 2020

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7 March 2020

volume

82

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7 March 2020

issue

8

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7 March 2020

page(s)

1611-1623

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SAbDab: the structural antibody database

7 March 2020

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10 September 2017

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Progress in super long loop prediction.

10 September 2017

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10 September 2017

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10 September 2017

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A new clustering of antibody CDR loop conformations

10 September 2017

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10 September 2017

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

10 September 2017

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MolProbity: all-atom structure validation for macromolecular crystallography

10 September 2017

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Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

10 September 2017

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Design of therapeutic proteins with enhanced stability.

10 September 2017

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RosettaAntibody: antibody variable region homology modeling server

10 September 2017

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Managing protein flexibility in docking and its applications

10 September 2017

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

10 September 2017

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PIGS: automatic prediction of antibody structures

10 September 2017

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

10 September 2017

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Affinity maturation of antibodies assisted by in silico modeling.

10 September 2017

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Flexible ligand docking to multiple receptor conformations: a practical alternative

10 September 2017

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10 September 2017

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Computational design of antibody-affinity improvement beyond in vivo maturation

10 September 2017

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Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design

10 September 2017

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10 September 2017

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Modeling structurally variable regions in homologous proteins with rosetta.

10 September 2017

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Expressed murine and human CDR-H3 intervals of equal length exhibit distinct repertoires that differ in their amino acid composition and predicted range of structures

10 September 2017

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10 September 2017

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Contributions of CDR3 to V H H domain stability and the design of monobody scaffolds for naive antibody libraries

10 September 2017

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

10 September 2017

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Analysis of the antigen combining site: correlations between length and sequence composition of the hypervariable loops and the nature of the antigen

10 September 2017

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

10 September 2017

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10 September 2017

The Protein Data Bank

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Standard conformations for the canonical structures of immunoglobulins

10 September 2017

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Conformations of immunoglobulin hypervariable regions

10 September 2017

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10 September 2017

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Antibodies as a model system for comparative model refinement.

10 September 2017

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Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex

25 September 2017

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Structure-based design of supercharged, highly thermoresistant antibodies

15 June 2018

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15 June 2018

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Antibody-antigen interactions: contact analysis and binding site topography.

15 June 2018

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

15 June 2018

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Antibody and antigen contact residues define epitope and paratope size and structure

15 June 2018

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The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops

21 August 2018

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21 August 2018

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Structural repertoire of immunoglobulin λ light chains

21 August 2018

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21 August 2018

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21 August 2018

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21 August 2018

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Improving the species cross-reactivity of an antibody using computational design

21 August 2018

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Structural classification of CDR-H3 revisited: a lesson in antibody modeling

21 August 2018

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Analyzing the "degree of humanness" of antibody sequences.

21 August 2018

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Shapes of antibody binding sites: qualitative and quantitative analyses based on a geomorphic classification scheme

21 August 2018

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Antibody variable regions: toward a unified modeling method.

21 August 2018

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Junctional amino acids determine the maturation pathway of an antibody.

21 August 2018

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Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics simulation.

21 August 2018

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

21 August 2018

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Rapid comparison of protein structures

21 August 2018

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Accurate bond and angle parameters for X-ray protein structure refinement

21 January 2018

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Multistate approaches in computational protein design

21 January 2018

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Developability index: a rapid in silico tool for the screening of antibody aggregation propensity

21 January 2018

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12 December 2020

A systematic comparison of free and bound antibodies reveals binding-related conformational changes

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12 December 2020

Canonical structures for the hypervariable regions of immunoglobulins

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12 December 2020

Structural classification of CDR-H3 in antibodies

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12 December 2020

Structural determinants in the sequences of immunoglobulin variable domain

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12 December 2020

Systematic classification of CDR-L3 in antibodies: implications of the light chain subtypes and the VL-VH interface

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12 December 2020

Identifiers

DOI

10.1002/PROT.24534

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24519881%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24519881%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

PubMed publication ID

24519881

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24519881%20AND%20SRC:MED&resulttype=core&format=json