Nature Search

Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains

Roland L. Dunbrack Jr
Martin Karplus
Research01 May 1994
Nature Structural Biology

Volume: 1, P: 334-340
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling

Qiang Wang
Adrian A Canutescu
Roland L Dunbrack Jr
Protocols06 Nov 2008
Nature Protocols

Volume: 3, P: 1832-1847
Macromolecular modeling and design in Rosetta: recent methods and frameworks

This Perspective reviews tools developed over the past five years in the macromolecular modeling, docking and design software Rosetta.

Julia Koehler Leman
Brian D. Weitzner
Richard Bonneau
Reviews01 Jun 2020
Nature Methods

Volume: 17, P: 665-680
Mutational dissection of a hole hopping route in a lytic polysaccharide monooxygenase (LPMO)

Lytic polysaccharide monooxygenases (LPMOs) are mono copper enzymes with outstanding industrial applicability. Here, the authors investigate the “hole hopping” mechanism in a bacterial LPMO and show that a strictly conserved tryptophan is critical for radical formation and hole transference, as well as reveal a correlation between the efficiency of hole transference and enzyme performance under oxidative stress.

Iván Ayuso-Fernández
Tom Z. Emrich-Mills
Vincent G. H. Eijsink
ResearchOpen Access10 May 2024
Nature Communications

Volume: 15, P: 1-15
Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth

Using somatic genome editing and Tuba-seq, Tang et al. uncover a previously uncharacterized role for HRAS and NRAS in impairing KRAS–KRAS interaction to suppress lung tumour growth.

Rui Tang
Emily G. Shuldiner
Monte M. Winslow
Research12 Jan 2023
Nature Cell Biology

Volume: 25, P: 159-169
ProtCID: a data resource for structural information on protein interactions

The authors previously developed the Protein Common Interface Database (ProtCID), which compares and clusters the interfaces of pairs of full-length protein chains with defined Pfam domain architectures in different PDB entries to identify biological assemblies. Here the authors extend ProtCID to the clustering of domain-domain interactions that also allows analyzing domain interactions with peptides, nucleic acids, and ligands.

Qifang Xu
Roland L. Dunbrack Jr.
ResearchOpen Access05 Feb 2020
Nature Communications

Volume: 11, P: 1-16
E proteins control the development of NKγδT cells through their invariant T cell receptor

Although normal γδ T cell development depends on the E protein antagonist, Id3, Id3 deficiency produces different phenotypes in distinct γδ T cell subsets. Here, the authors demonstrate that Id3 deficiency impairs the development of Vγ3⁺ T cells, while promoting that of NKγδT cells expressing the invariant Vγ1Vδ6.3 TCR.

Ariana Mihai
Sang-Yun Lee
David L. Wiest
ResearchOpen Access13 Jun 2024
Nature Communications

Volume: 15, P: 1-14
FAM122A ensures cell cycle interphase progression and checkpoint control by inhibiting B55α/PP2A through helical motifs

FAM122A is required for timely progression through the G0/G1 transition and checkpoint integrity. Here, the authors report the mechanism by which FAM122A inhibits the major B55α/PP2A Ser/Thr phosphatase using adjacent helices that dock on B55α and occlude the active site of PP2A/C.

Jason S. Wasserman
Bulat Faezov
Xavier Graña
ResearchOpen Access10 Jul 2024
Nature Communications

Volume: 15, P: 1-20
MOLECULAR MODELING OF PHOSPHOFRUCTOKINASE FROM ENTAMOEBA HISTOLYTICA FOR THE PREDICTION OF NEW ANTIPARASITIC AGENTS. • 992

Carrie L Byington
Roland L Dunbrack Jr.
Nina Agabian
Research01 Apr 1996
Pediatric Research

Volume: 39, P: 168
A scoundrel's refuge

Roland L Dunbrack Jr
Books & Arts01 Aug 2003
Nature Structural & Molecular Biology

Volume: 10, P: 590
Rapid calcium-dependent activation of Aurora-A kinase

Aurora-A kinase localizes to centrosomes, is involved in the progression through mitosis and is overexpressed in certain cancers. Here, calcium is shown to induce Aurora-A auto-phosphorylation in a calmodulin-dependent manner, suggesting a novel role for Aurora-A in non-mitotic cells.

Olga V. Plotnikova
Elena N. Pugacheva
Erica A. Golemis
ResearchOpen Access07 Sept 2010
Nature Communications

Volume: 1, P: 1-8
Structure of a human ASF1a–HIRA complex and insights into specificity of histone chaperone complex assembly

Yong Tang
Maxim V Poustovoitov
Ronen Marmorstein
Research17 Sept 2006
Nature Structural & Molecular Biology

Volume: 13, P: 921-929
A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains

Vivek Modi
Roland L. Dunbrack Jr.
ResearchOpen Access24 Dec 2019
Scientific Reports

Volume: 9, P: 1-16
Modeling and docking of antibody structures with Rosetta

Weitzner et al. describe a computational protocol that uses RosettaAntibody to predict antibody structures from sequence data. SnugDock is then used for docking of these structures to protein antigens.

Brian D Weitzner
Jeliazko R Jeliazkov
Jeffrey J Gray
Protocols26 Jan 2017
Nature Protocols

Volume: 12, P: 401-416

Search

Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains

SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Mutational dissection of a hole hopping route in a lytic polysaccharide monooxygenase (LPMO)

Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth

ProtCID: a data resource for structural information on protein interactions

E proteins control the development of NKγδT cells through their invariant T cell receptor

FAM122A ensures cell cycle interphase progression and checkpoint control by inhibiting B55α/PP2A through helical motifs

MOLECULAR MODELING OF PHOSPHOFRUCTOKINASE FROM ENTAMOEBA HISTOLYTICA FOR THE PREDICTION OF NEW ANTIPARASITIC AGENTS. • 992

A scoundrel's refuge

Rapid calcium-dependent activation of Aurora-A kinase

Structure of a human ASF1a–HIRA complex and insights into specificity of histone chaperone complex assembly

A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains

Modeling and docking of antibody structures with Rosetta

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