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)
RosettaDDGPrediction for high-throughput mutational scans: From stability to binding
Valentina Sora et al.
PROTEIN SCIENCE (2023)
Inhibition of p53 protein aggregation as a cancer treatment strategy
Kalvin Kwan et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2023)
Transient exposure of a buried phosphorylation site in an autoinhibited protein
Simone Orioli et al.
BIOPHYSICAL JOURNAL (2022)
Harder, better, faster, stronger: Large-scale QM and QM/MM for predictive modeling in enzymes and proteins
Vyshnavi Vennelakanti et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2022)
PROTAC targeted protein degraders: the past is prologue
Miklos Bekes et al.
NATURE REVIEWS DRUG DISCOVERY (2022)
dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications
Zhongyan Li et al.
NUCLEIC ACIDS RESEARCH (2022)
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
Mihaly Varadi et al.
NUCLEIC ACIDS RESEARCH (2022)
MutateX: an automated pipeline for in silico saturation mutagenesis of protein structures and structural ensembles
Matteo Tiberti et al.
BRIEFINGS IN BIOINFORMATICS (2022)
Cancer-related Mutations with Local or Long-range Effects on an Allosteric Loop of p53
Kristine Degn et al.
JOURNAL OF MOLECULAR BIOLOGY (2022)
Integration of experimental data and use of automated fitting methods in developing protein force fields
Marcelo D. Poleto et al.
COMMUNICATIONS CHEMISTRY (2022)
A structural biology community assessment of AlphaFold2 applications
Mehmet Akdel et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2022)
Deciphering the Path of S-nitrosation of Human Thioredoxin: Evidence of an Internal NO Transfer and Implication for the Cellular Responses to NO
Vitor S. Almeida et al.
ANTIOXIDANTS (2022)
The Cancermuts software package for the prioritization of missense cancer variants: a case study of AMBRA1 in melanoma
Matteo Tiberti et al.
CELL DEATH & DISEASE (2022)
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins
Neha Kalmankar et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2022)
Targeting methionine aminopeptidase 2 in cancer, obesity, and autoimmunity
Andrea Goya Grocin et al.
TRENDS IN PHARMACOLOGICAL SCIENCES (2021)
Clathrin: the molecular shape shifter
Katherine M. Wood et al.
BIOCHEMICAL JOURNAL (2021)
Protein S-nitrosylation and oxidation contribute to protein misfolding in neurodegeneration
Tomohiro Nakamura et al.
FREE RADICAL BIOLOGY AND MEDICINE (2021)
The molecular chaperone TRAP1 in cancer: From the basics of biology to pharmacological targeting
Ionica Masgras et al.
SEMINARS IN CANCER BIOLOGY (2021)
ClinVar: improvements to accessing data
Melissa J. Landrum et al.
NUCLEIC ACIDS RESEARCH (2020)
S-nitrosylation affects TRAP1 structure and ATPase activity and modulates cell response to apoptotic stimuli
Fiorella Faienza et al.
BIOCHEMICAL PHARMACOLOGY (2020)
Rational Design of Allosteric and Selective Inhibitors of the Molecular Chaperone TRAP1
Carlos Sanchez-Martin et al.
CELL REPORTS (2020)
Exploiting S-nitrosylation for cancer therapy: facts and perspectives
Salvatore Rizza et al.
BIOCHEMICAL JOURNAL (2020)
Protein Dynamics Enables Phosphorylation of Buried Residues in Cdk2/Cyclin-A-Bound p27
Joao Henriques et al.
BIOPHYSICAL JOURNAL (2020)
Prediction of Protein Mutational Free Energy: Benchmark and Sampling Improvements Increase Classification Accuracy
Brandon Frenz et al.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)
FoldX 5.0: working with RNA, small molecules and a new graphical interface
Javier Delgado et al.
BIOINFORMATICS (2019)
Importance of the Force Field Choice in Capturing Functionally Relevant Dynamics in the von Willebrand Factor
Antonija Kuzmanic et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2019)
S-nitrosylation and its role in breast cancer angiogenesis and metastasis
Pamela Ehrenfeld et al.
NITRIC OXIDE-BIOLOGY AND CHEMISTRY (2019)
COSMIC: the Catalogue Of Somatic Mutations In Cancer
John G. Tate et al.
NUCLEIC ACIDS RESEARCH (2019)
Dynamics-based community analysis and perturbation response scanning of allosteric interaction networks in the TRAP1 chaperone structures dissect molecular linkage between conformational asymmetry and sequential ATP hydrolysis
Gennady M. Verkhivker
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2018)
ClinVar Miner: Demonstrating utility of a Web-based tool for viewing and filtering ClinVar data
Alex Henrie et al.
HUMAN MUTATION (2018)
The Structural Asymmetry of Mitochondrial Hsp90 (Trap1) Determines Fine Tuning of Functional Dynamics
Elisabetta Moroni et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
Cand1-Mediated Adaptive Exchange Mechanism Enables Variation in F-Box Protein Expression
Xing Liu et al.
MOLECULAR CELL (2018)
Evidence against Stable Protein S-Nitrosylation as a Widespread Mechanism of Post-translational Regulation
Kathryn Wolhuter et al.
MOLECULAR CELL (2018)
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures
Aleksander Kuriata et al.
NUCLEIC ACIDS RESEARCH (2018)
How well do force fields capture the strength of salt bridges in proteins?
Mustapha Carab Ahmed et al.
PEERJ (2018)
Computational Structural Biology of S-nitrosylation of Cancer Targets
Emmanuelle Bignon et al.
FRONTIERS IN ONCOLOGY (2018)
The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers
Zbyslaw Sondka et al.
NATURE REVIEWS CANCER (2018)
Click-PEGylation - A mobility shift approach to assess the redox state of cysteines in candidate proteins
Lucie A. G. van Leeuwen et al.
FREE RADICAL BIOLOGY AND MEDICINE (2017)
Chronicles of a reductase: Biochemistry, genetics and physio-pathological role of GSNOR
Salvatore Rizza et al.
FREE RADICAL BIOLOGY AND MEDICINE (2017)
How widespread is stable protein S-nitrosylation as an end-effector of protein regulation?
Kathryn Wolhuter et al.
FREE RADICAL BIOLOGY AND MEDICINE (2017)
Broad Analysis of Vicinal Disulfides: Occurrences, Conformations with Cis or with Trans Peptides, and Functional Roles Including Sugar Binding
Jane S. Richardson et al.
JOURNAL OF MOLECULAR BIOLOGY (2017)
Coexpression of NOS2 and COX2 accelerates tumor growth and reduces survival in estrogen receptor-negative breast cancer
Debashree Basudhar et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
The Chaperone TRAP1 As a Modulator of the Mitochondrial Adaptations in Cancer Cells
Ionica Masgras et al.
FRONTIERS IN ONCOLOGY (2017)
Altered S-nitrosothiol homeostasis provides a survival advantage to breast cancer cells in HER2 tumors and reduces their sensitivity to trastuzumab
Amanda Canas et al.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2016)
Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules
Hahnbeom Park et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Maxim V. Kuleshov et al.
NUCLEIC ACIDS RESEARCH (2016)
S-nitrosylation of XIAP at Cys 213 of BIR2 domain impairs XIAP's anti-caspase 3 activity and anti-apoptotic function
Weiwei Wu et al.
APOPTOSIS (2015)
The basics of thiols and cysteines in redox biology and chemistry
Leslie B. Poole
FREE RADICAL BIOLOGY AND MEDICINE (2015)
Comparing Molecular Dynamics Force Fields in the Essential Subspace
Fernando Martin-Garcia et al.
PLOS ONE (2015)
Protein disulfide engineering
Alan A. Dombkowski et al.
FEBS LETTERS (2014)
PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins
Matteo Tiberti et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)
Conformational Changes and Free Energies in a Proline Isomerase
Elena Papaleo et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Protein Microarray Characterization of the S-Nitrosoproteome
Yun-Il Lee et al.
MOLECULAR & CELLULAR PROTEOMICS (2014)
ClinVar: public archive of relationships among sequence variation and human phenotype
Melissa J. Landrum et al.
NUCLEIC ACIDS RESEARCH (2014)
Protein Flexibility and Cysteine Reactivity: Influence of Mobility on the H-Bond Network and Effects on pKa Prediction
Stefano M. Marino
PROTEIN JOURNAL (2014)
A gene signature based method for identifying subtypes and subtype-specific drivers in cancer with an application to medulloblastoma
Peikai Chen et al.
BMC BIOINFORMATICS (2013)
Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal
Jianjiong Gao et al.
SCIENCE SIGNALING (2013)
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
Christopher D. Wassman et al.
NATURE COMMUNICATIONS (2013)
The PEG-switch assay: A fast semi-quantitative method to determine protein reversible cysteine oxidation
Joseph Robert Burgoyne et al.
JOURNAL OF PHARMACOLOGICAL AND TOXICOLOGICAL METHODS (2013)
A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications
Drazen Petrov et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
Analysis and Functional Prediction of Reactive Cysteine Residues
Stefano M. Marino et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2012)
OPM database and PPM web server: resources for positioning of proteins in membranes
Mikhail A. Lomize et al.
NUCLEIC ACIDS RESEARCH (2012)
Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank
Robbie P. Joosten et al.
BIOINFORMATICS (2011)
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions
Mats H. M. Olsson et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Disulfide Bond Acquisition through Eukaryotic Protein Evolution
Jason W. H. Wong et al.
MOLECULAR BIOLOGY AND EVOLUTION (2011)
Site-specific and redox-controlled S-nitrosation of thioredoxin
Katherine T. Barglow et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Site-Specific Proteomics Approach for Study Protein S-Nitrosylation
Miao Liu et al.
ANALYTICAL CHEMISTRY (2010)
Structural Analysis of Cysteine S-Nitrosylation: A Modified Acid-Based Motif and the Emerging Role of Trans-Nitrosylation
Stefano M. Marino et al.
JOURNAL OF MOLECULAR BIOLOGY (2010)
Cysteine Function Governs Its Conservation and Degeneration and Restricts Its Utilization on Protein Surfaces
Stefano M. Marino et al.
JOURNAL OF MOLECULAR BIOLOGY (2010)
Redox Regulatory Mechanism of Transnitrosylation by Thioredoxin
Changgong Wu et al.
MOLECULAR & CELLULAR PROTEOMICS (2010)
Transnitrosylation of XIAP Regulates Caspase-Dependent Neuronal Cell Death
Tomohiro Nakamura et al.
MOLECULAR CELL (2010)
Stabilization of mutant p53 via alkylation of cysteines and effects on DNA binding
Joel L. Kaar et al.
PROTEIN SCIENCE (2010)
Improved side-chain torsion potentials for the Amber ff99SB protein force field
Kresten Lindorff-Larsen et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
S-Nitrosylation from GSNOR Deficiency Impairs DNA Repair and Promotes Hepatocarcinogenesis
Wei Wei et al.
SCIENCE TRANSLATIONAL MEDICINE (2010)
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
Massimiliano Bonomi et al.
COMPUTER PHYSICS COMMUNICATIONS (2009)
Proteomic analysis of S-nitrosylation and denitrosylation by resin-assisted capture
Michael T. Forrester et al.
NATURE BIOTECHNOLOGY (2009)
S-nitrosylation of XIAP compromises neuronal survival in Parkinson's disease
Anthony H. K. Tsang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Force field parameters for S-nitrosocysteine and molecular dynamics simulations of S-nitrosated thioredoxin
Sanghwa Han
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2008)
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
Berk Hess et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Well-tempered metadynamics: A smoothly converging and tunable free-energy method
Alessandro Barducci et al.
PHYSICAL REVIEW LETTERS (2008)
How similar are amino acid mutations in human genetic diseases and evolution
Hao Wu et al.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2007)
Thioredoxin is required for S-nitrosation of procaspase-3 and the inhibition of apoptosis in Jurkat cells
Douglas A. Mitchell et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Evaluating the stability of disulfide bridges in proteins: a torsional potential energy surface for diethyl disulfide
N. L. Haworth et al.
MOLECULAR SIMULATION (2007)
Allosteric disulfide bonds
Bryan Schmidt et al.
BIOCHEMISTRY (2006)
Mapping PDB chains to UniProtKB entries
ACR Martin
BIOINFORMATICS (2005)
Reactivation of mutant p53 and induction of apoptosis in human tumor cells by maleimide analogs
VJN Bykov et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2005)
Thioredoxin catalyzes the S-nitrosation of the caspase-3 active site cysteine
DA Mitchell et al.
NATURE CHEMICAL BIOLOGY (2005)
A universal trend of amino acid gain and loss in protein evolution
IK Jordan et al.
NATURE (2005)
Protein S-nitrosylation:: Purview and parameters
DT Hess et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2005)
NEDD8 modification of CUL1 short article dissociates p120CAND1, an inhibitor of CULl-SKP1 binding and SCIF ligases
JD Liu et al.
MOLECULAR CELL (2002)
Nitrosylation: The prototypic redox-based signaling mechanism
JS Stamler et al.
CELL (2001)
Structural basis of caspase-7 inhibition by XIAP
JJ Chai et al.
CELL (2001)