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Structure-based cross-docking analysis of antibody-antigen interactions

autor

Jeffrey J. Gray

Krishna Praneeth Kilambi

opublikowano w: Scientific Reports

data publikacji: 2017-08-15

język: język angielski

Cites articles 34

Data

Tytuł

Autorzy

2016-12-21

Temporal stability and molecular persistence of the bone marrow plasma cell antibody repertoire

Edward Marcotte, Gregory C Ippolito
2016-11-07

Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination

Ted Ross, Daechan Park, Gregory C Ippolito, John R. Mascola, Chang-Han Lee, Florian Krammer, George Georgiou, Andrew D Ellington, Stephen Quake, Peter D. Kwong, Brandon J DeKosky, Yaroslav Tsybovsky, Jiwon Lee, Lingshu Wang, Wing-Pui Kong, M Gordon Joyce, Paul G. Thomas, Jason J Lavinder, Kwanyee Leung, Aliaksandr Druz, Daniel R. Boutz, Cornelia L Dekker
2016-11-07

Influenza immunization elicits antibodies specific for an egg-adapted vaccine strain

Jiwon Lee, Goran Bajic, Gregory C Ippolito, Philip R Dormitzer, Stephen C. Harrison, Barton Haynes, Thomas B. Kepler, Pirada Suphaphiphat, Ethan C Settembre, M Anthony Moody, Hua-Xin Liao
2016-08-25

Pushing the Backbone in Protein-Protein Docking

Daisuke Kuroda
2016-04-25

Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

Daechan Park, Daisuke Kuroda, Gregory C Ippolito, Brandon J DeKosky
2016-02-04

Ultra-high-throughput sequencing of the immune receptor repertoire from millions of lymphocytes

George Georgiou, Andrew D Ellington, Brandon J DeKosky
2015-07-29

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

Iain H Moal, Anna Vangone, Brian G Pierce, Panagiotis L. Kastritis, Mieczysław Torchała, Brian Jimenez, Paul A. Bates, Juan Fernández-Recio, Alexandre Bonvin, Thom Vreven
2015-02-10

Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta

Tanja Kortemme, Amelie Stein, Jack Snoeyink, David Baker, Brian Kuhlman, Andrew Leaver-Fay
2014-12-11

Protein-protein docking with dynamic residue protonation states

Krishna Praneeth Kilambi
2014-03-31

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

Brian D Weitzner, Daisuke Kuroda
2014-09-02

CCharPPI web server: computational characterization of protein-protein interactions from structure

Iain H Moal, Brian Jimenez, Juan Fernández-Recio
2013

Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information

Sophie Sacquin-Mora, Yann Ponty, Alessandra Carbone
2013-10-17

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27

Ora Schueler-Furman, Krishna Praneeth Kilambi, Daisuke Kuroda, Jeffrey J. Gray, Richard Bonneau
2011-09-29

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

Chaok Seok, Ora Schueler-Furman, Mayuko Takeda-Shitaka, Shoshana Wodak, Takashi Ishida, Carles Pons, Charles H. Robert, Panagiotis L. Kastritis, Iain H Moal, Brian G Pierce, Yuedong Yang, Jeffrey J. Gray, Sarel J Fleishman, Juan Fernández-Recio, Paul A. Bates, Huan-Xiang Zhou, Yaoqi Zhou, David Baker, Vladimir Potapov, Julie Bernauer, Xianjin Xu, Nir London, Masahito Ohue, Pemra Özbek, Haruki Nakamura, Daisuke Kihara, Martin Zacharias, Thom Vreven, Brian Kuhlman, Alexander Tropsha, Joël Janin, Türkan Haliloğlu, Timothy A Whitehead, Hahnbeom Park, Hasup Lee
2011-08-02

Benchmarking and analysis of protein docking performance in Rosetta v3.2.

Brian D Weitzner, Jeffrey J. Gray
2011-03

A structure-based benchmark for protein-protein binding affinity

Alexandre Bonvin, Panagiotis L. Kastritis, Iain H Moal, Paul A. Bates, Joël Janin
2011-09-07

Protein-protein binding affinity prediction on a diverse set of structures

Iain H Moal, Paul A. Bates
2010-08-29

Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells

Xin Ge, George Georgiou, Andrew D Ellington
2010-05-07

Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark

Alexandre Bonvin, Panagiotis L. Kastritis
2010-01-22

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

Jeffrey J. Gray
2009-10-29

Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire

David R. Cox
2009-05-20

RosettaAntibody: antibody variable region homology modeling server

Jeffrey J. Gray
2009-05-01

High-throughput sequencing of the zebrafish antibody repertoire

Ning Jiang, Stephen Quake, Daniel S. Fisher
2008-05-24

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

Jeffrey J. Gray
2008-05-09

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

Yuedong Yang, Yaoqi Zhou
2008-07-01

A combination of rescoring and refinement significantly improves protein docking performance
2007-11-19

OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing.
2007-10-01

FireDock: fast interaction refinement in molecular docking.

Ruth Nussinov, Haim Wolfson, Nelly Andrusier
2003-02-01

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

David Baker, Tanja Kortemme
1999-05-01

Effective energy function for proteins in solution

Martin Karplus
1999-01-01

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

David Baker, Charles Kooperberg, Brian A. Fox
1997-08-01

Bayesian statistical analysis of protein side-chain rotamer preferences

Fred E Cohen, Roland Dunbrack

Artykuł - wd:Q41421607

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