Related references
Note: Only part of the references are listed.AlphaFill: enriching AlphaFold models with ligands and cofactors
Maarten L. Hekkelman et al.
NATURE METHODS (2023)
Protein degraders enter the clinic - a new approach to cancer therapy
Deborah Chirnomas et al.
NATURE REVIEWS CLINICAL ONCOLOGY (2023)
Structures of BIRC6-client complexes provide a mechanism of SMAC-mediated release of caspases
Moritz Hunkeler et al.
SCIENCE (2023)
Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs
Nan Bai et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2022)
Phase 1/2 study of ARV-110, an androgen receptor (AR) PROTAC degrader, in metastatic castration-resistant prostate cancer (mCRPC).
Xin Gao et al.
JOURNAL OF CLINICAL ONCOLOGY (2022)
The PROTAC gold rush
Ken Garber
NATURE BIOTECHNOLOGY (2022)
PROTAC targeted protein degraders: the past is prologue
Miklos Bekes et al.
NATURE REVIEWS DRUG DISCOVERY (2022)
First-in-human safety and activity of ARV-471, a novel PROTAC (R) estrogen receptor degrader, in ER+/HER2-locally advanced or metastatic breast cancer
Erika Hamilton et al.
CANCER RESEARCH (2022)
Are transient protein-protein interactions more dispensable?
Mohamed Ali Ghadie et al.
PLOS COMPUTATIONAL BIOLOGY (2022)
Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry
Tom Dixon et al.
NATURE COMMUNICATIONS (2022)
PROTACs: great opportunities for academia and industry (an update from 2020 to 2021)
Ming He et al.
SIGNAL TRANSDUCTION AND TARGETED THERAPY (2022)
PROTAC-DB: an online database of PROTACs
Gaoqi Weng et al.
NUCLEIC ACIDS RESEARCH (2021)
Snapshots and ensembles of BTK and cIAP1 protein degrader ternary complexes
James Schiemer et al.
NATURE CHEMICAL BIOLOGY (2021)
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences
Stephen K. Burley et al.
NUCLEIC ACIDS RESEARCH (2021)
Using normal mode analysis on protein structural models. How far can we go on our predictions?
Nuria Cirauqui Diaz et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2021)
Integrative Modeling of PROTAC-Mediated Ternary Complexes
Gaoqi Weng et al.
JOURNAL OF MEDICINAL CHEMISTRY (2021)
AlphaFold heralds a data-driven revolution in biology and medicine
Janet M. Thornton et al.
NATURE MEDICINE (2021)
The trRosetta server for fast and accurate protein structure prediction
Zongyang Du et al.
NATURE PROTOCOLS (2021)
Antibody-Mediated Delivery of Chimeric BRD4 Degraders. Part 2: Improvement of In Vitro Antiproliferation Activity and In Vivo Antitumor Efficacy
Peter S. Dragovich et al.
JOURNAL OF MEDICINAL CHEMISTRY (2021)
A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models
Xufen Yu et al.
SCIENCE TRANSLATIONAL MEDICINE (2021)
Discovery and Characterisation of Highly Cooperative FAK-Degrading PROTACs
Robert P. Law et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)
Acute pharmacological degradation of Helios destabilizes regulatory T cells
Eric S. Wang et al.
NATURE CHEMICAL BIOLOGY (2021)
Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations
Wei Zheng et al.
CELL REPORTS METHODS (2021)
LightDock goes information-driven
Jorge Roel-Touris et al.
BIOINFORMATICS (2020)
Design, synthesis and biological evaluation of Proteolysis Targeting Chimeras (PROTACs) as a BTK degraders with improved pharmacokinetic properties
Saul Jaime-Figueroa et al.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2020)
Discovery of Potent and Selective Epidermal Growth Factor Receptor (EGFR) Bifunctional Small-Molecule Degraders
Meng Cheng et al.
JOURNAL OF MEDICINAL CHEMISTRY (2020)
Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI rounds 37-45
Shourya S. Roy Burman et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2020)
Structural Insights into PROTAC-Mediated Degradation of BcI-xL
Chun-wa Chung et al.
ACS CHEMICAL BIOLOGY (2020)
PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes
Daniel Zaidman et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via New In Silico Methodologies
Michael L. Drummond et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
CC-90009, a novel cereblon E3 ligase modulator targets acute myeloid leukemia blasts and leukemia stem cells
Christine Surka et al.
BLOOD (2020)
Pan-SMARCA/PB1 Bromodomain Inhibitors and Their Role in Regulating Adipogenesis
Marek Wanior et al.
JOURNAL OF MEDICINAL CHEMISTRY (2020)
Integrative modeling of membrane-associated protein assemblies
Jorge Roel-Touris et al.
NATURE COMMUNICATIONS (2020)
Exploring Targeted Degradation Strategy for Oncogenic KRASG12C
Mei Zeng et al.
CELL CHEMICAL BIOLOGY (2020)
In Silico Modeling of PROTAC-Mediated Ternary Complexes: Validation and Application
Michael L. Drummond et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)
Extensive benchmark of rDock as a peptide-protein docking tool
Daniel Soler et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2019)
BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design
William Farnaby et al.
NATURE CHEMICAL BIOLOGY (2019)
Assessing the performance of MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein-peptide complexes
Gaoqi Weng et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2019)
Identification and Characterization of Von Hippel-Lindau-Recruiting Proteolysis Targeting Chimeras (PROTACs) of TANK-Binding Kinase 1
Andrew P. Crew et al.
JOURNAL OF MEDICINAL CHEMISTRY (2018)
A Cereblon Modulator (CC-220) with Improved Degradation of Ikaros and Aiolos
Mary E. Matyskiela et al.
JOURNAL OF MEDICINAL CHEMISTRY (2018)
Efficient flexible backbone protein-protein docking for challenging targets
Nicholas A. Marze et al.
BIOINFORMATICS (2018)
Protein structure-based drug design: from docking to molecular dynamics
Pawel Sledz et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)
Plasticity in binding confers selectivity in ligand-induced protein degradation
Radoslaw P. Nowak et al.
NATURE CHEMICAL BIOLOGY (2018)
Modeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry
Joshua Matthew Allen Bullock et al.
STRUCTURE (2018)
An Ion-Permeable State of the Glycine Receptor Captured by Molecular Dynamics
Adrien Henri Cerdan et al.
STRUCTURE (2018)
LightDock: a new multi-scale approach to protein-protein docking
Brian Jimenez-Garcia et al.
BIOINFORMATICS (2018)
Structural basis of PROTAC cooperative recognition for selective protein degradation
Morgan S. Gadd et al.
NATURE CHEMICAL BIOLOGY (2017)
Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry
Devin K. Schweppe et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
VoroMQA: Assessment of protein structure quality using interatomic contact areas
Kliment Olechnovic et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2017)
Modular PROTAC Design for the Degradation of Oncogenic BCR-ABL
Ashton C. Lai et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2016)
FRODOCK 2.0: fast protein-protein docking server
Erney Ramirez-Aportela et al.
BIOINFORMATICS (2016)
Predicting Protein-Protein Interactions from the Molecular to the Proteome Level
Ozlem Keskin et al.
CHEMICAL REVIEWS (2016)
A novel cereblon modulator recruits GSPT1 to the CRL4CRBN ubiquitin ligase
Mary E. Matyskiela et al.
NATURE (2016)
DockQ: A Quality Measure for Protein-Protein Docking Models
Sankar Basu et al.
PLOS ONE (2016)
Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system
Mainak Guharoy et al.
NATURE COMMUNICATIONS (2016)
Catalytic in vivo protein knockdown by small-molecule PROTACs
Daniel P. Bondeson et al.
NATURE CHEMICAL BIOLOGY (2015)
Docking, scoring, and affinity prediction in CAPRI
Marc F. Lensink et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2013)
Protein-protein interaction networks: probing disease mechanisms using model systems
Uros Kuzmanov et al.
GENOME MEDICINE (2013)
Software News and Updates MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations
Naveen Michaud-Agrawal et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
Transient proteinprotein interactions
Saliha Ece Acuner Ozbabacan et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2011)
A Multidomain Flexible Docking Approach to Deal with Large Conformational Changes in the Modeling of Biomolecular Complexes
Ezgi Karaca et al.
STRUCTURE (2011)
Predicting Continuous Local Structure and the Effect of Its Substitution for Secondary Structure in Fragment-Free Protein Structure Prediction
Eshel Faraggi et al.
STRUCTURE (2009)
The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation
Jin Liu et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
Structural and biochemical bases for the inhibition of autophagy and apoptosis by viral BCL-2 of murine γ-herpesvirus 68
Bonsu Ku et al.
PLOS PATHOGENS (2008)
pyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
Tammy Man-Kuang Cheng et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
Structural basis for molecular recognition and presentation of histone H3 By WDR5
Anja Schuetz et al.
EMBO JOURNAL (2006)
Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function
C Zhang et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
Protein-protein interactions in human disease
DP Ryan et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2005)
Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
R Méndez et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
JJ Gray et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
ZDOCK: An initial-stage protein-docking algorithm
R Chen et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)
HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
C Dominguez et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Protacs: Chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation
KM Sakamoto et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Activation of HIF1α ubiquitination by a reconstituted von Hippel-Lindau (VHL) tumor suppressor complex
T Kamura et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)