Novel sampling strategies and a coarse‐grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI rounds 37–45

Flexible Backbone Assembly and Refinement of Symmetrical Homomeric Complexes

(2019) Shourya S. Roy Burman et al.   STRUCTURE

Efficient flexible backbone protein–protein docking for challenging targets

(2018) Nicholas A Marze et al.   BIOINFORMATICS

Helicobacter pylori adhesin HopQ disrupts trans dimerization in human CEACAMs

(2018) Kristof Moonens et al.   EMBO JOURNAL

Structural Activation of Pro-inflammatory Human Cytokine IL-23 by Cognate IL-23 Receptor Enables Recruitment of the Shared Receptor IL-12Rβ1

(2018) Yehudi Bloch et al.   IMMUNITY

Insc:LGN tetramers promote asymmetric divisions of mammary stem cells

(2018) Simone Culurgioni et al.   Nature Communications

Ultrahigh specificity in a network of computationally designed protein-interaction pairs

(2018) Ravit Netzer et al.   Nature Communications

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

CH/π Interactions in Carbohydrate Recognition

(2017) Vojtěch Spiwok   MOLECULES

Modeling and docking of antibody structures with Rosetta

(2017) Brian D Weitzner et al.   Nature Protocols

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

The challenge of modeling protein assemblies: the CASP12-CAPRI experiment

(2017) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assembly of Ruminococcus flavefaciens cellulosome revealed by structures of two cohesin-dockerin complexes

(2017) Pedro Bule et al.   Scientific Reports

Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking

(2016) Anita K. Nivedha et al.   Journal of Chemical Theory and Computation

Residue-centric modeling and design of saccharide and glycoconjugate structures

(2016) Jason W. Labonte et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35

(2016) Nicholas A. Marze et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Crystal structure of raptor adenovirus 1 fibre head and role of the beta-hairpin in siadenovirus fibre head domains

(2016) Thanh H. Nguyen et al.   Virology Journal

Helicobacter pylori adhesin HopQ engages in a virulence-enhancing interaction with human CEACAMs

(2016) Anahita Javaheri et al.   Nature Microbiology

Crucial Roles of Single Residues in Binding Affinity, Specificity, and Promiscuity in the Cellulosomal Cohesin-Dockerin Interface

(2015) Michal Slutzki et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cell-surface Attachment of Bacterial Multienzyme Complexes Involves Highly Dynamic Protein-Protein Anchors

(2015) Kate Cameron et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Carbohydrate–Aromatic Interactions in Proteins

(2015) Kieran L. Hudson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein-Protein Docking: From Interaction to Interactome

(2014) Ilya A. Vakser   BIOPHYSICAL JOURNAL

Non-Canonical Interleukin 23 Receptor Complex Assembly

(2014) Jutta Schröder et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CEACAM1 regulates TIM-3-mediated tolerance and exhaustion

(2014) Yu-Hwa Huang et al.   NATURE

Crystal Structure of the Fibre Head Domain of the Atadenovirus Snake Adenovirus 1

(2014) Abhimanyu K. Singh et al.   PLoS One

Protein-Protein Docking with Dynamic Residue Protonation States

(2014) Krishna Praneeth Kilambi et al.   PLoS Computational Biology

Towards a detailed atlas of protein–protein interactions

(2013) Roberto Mosca et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein–protein interaction networks: the puzzling riches

(2013) Shoshana J Wodak et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

(2013) Amelie Stein et al.   PLoS One

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

(2013) Krishna Praneeth Kilambi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Full-Length Structure of a Sensor Histidine Kinase Pinpoints Coaxial Coiled Coils as Signal Transducers and Modulators

(2013) Ralph P. Diensthuber et al.   STRUCTURE

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

Structure of the Ultra-High-Affinity Colicin E2 DNase–Im2 Complex

(2012) Justyna Aleksandra Wojdyla et al.   JOURNAL OF MOLECULAR BIOLOGY

Analysis and Modeling of the Variable Region of Camelid Single-Domain Antibodies

(2011) A. Sircar et al.   JOURNAL OF IMMUNOLOGY

Structures of Iron-Dependent Alcohol Dehydrogenase 2 from Zymomonas mobilis ZM4 with and without NAD+ Cofactor

(2011) Ji-Hyun Moon et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase

(2011) Shinya Fushinobu et al.   NATURE

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

(2011) Po-Ssu Huang et al.   PLoS One

Crystal Structures of the Solute Receptor GacH of Streptomyces glaucescens in Complex with Acarbose and an Acarbose Homolog: Comparison with the Acarbose-Loaded Maltose-Binding Protein of Salmonella typhimurium

(2010) Ardeschir Vahedi-Faridi et al.   JOURNAL OF MOLECULAR BIOLOGY

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

(2010) Michael D. Tyka et al.   JOURNAL OF MOLECULAR BIOLOGY

SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

(2010) Aroop Sircar et al.   PLoS Computational Biology

Crystal structure of an inverting GH 43 1,5-α-L-arabinanase fromGeobacillus stearothermophiluscomplexed with its substrate

(2009) Anat Alhassid et al.   BIOCHEMICAL JOURNAL

Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles

(2008) Sidhartha Chaudhury et al.   JOURNAL OF MOLECULAR BIOLOGY

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction

(2008) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

How to Switch Off a Histidine Kinase: Crystal Structure of Geobacillus stearothermophilus KinB with the inhibitor Sda

(2008) Matthew J. Bick et al.   JOURNAL OF MOLECULAR BIOLOGY