标题
Benchmarking In Silico Tools for Cysteine pKa Prediction
作者
关键词
-
出版物
Journal of Chemical Information and Modeling
Volume 63, Issue 7, Pages 2170-2180
出版商
American Chemical Society (ACS)
发表日期
2023-03-31
DOI
10.1021/acs.jcim.3c00004
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Novel Lennard-Jones Parameters for Cysteine and Selenocysteine in the AMBER Force Field
- (2023) Federico N. Pedron et al. Journal of Chemical Information and Modeling
- Prediction of protein pKa with representation learning
- (2022) Hatice Gokcan et al. Chemical Science
- Protein pKa Prediction by Tree-Based Machine Learning
- (2022) Ada Y. Chen et al. Journal of Chemical Theory and Computation
- A Fast and Interpretable Deep Learning Approach for Accurate Electrostatics-Driven pKa Predictions in Proteins
- (2022) Pedro B.P.S. Reis et al. Journal of Chemical Theory and Computation
- Extending the Stochastic Titration CpHMD to CHARMM36m
- (2022) João G. N. Sequeira et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Mechanistic aspects of thiol additions to Michael acceptors: Insights from computations
- (2022) Ras Baizureen Roseli et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Modeling the Binding and Conformational Energetics of a Targeted Covalent Inhibitor to Bruton’s Tyrosine Kinase
- (2021) Ernest Awoonor-Williams et al. Journal of Chemical Information and Modeling
- Protein pKa Prediction with Machine Learning
- (2021) Zhitao Cai et al. ACS Omega
- Predicting Reactive Cysteines with Implicit-Solvent-Based Continuous Constant pH Molecular Dynamics in Amber
- (2020) Robert C. Harris et al. Journal of Chemical Theory and Computation
- Scalable molecular dynamics on CPU and GPU architectures with NAMD
- (2020) James C. Phillips et al. JOURNAL OF CHEMICAL PHYSICS
- PypKa: A Flexible Python Module for Poisson–Boltzmann-Based pKa Calculations
- (2020) Pedro B. P. S. Reis et al. Journal of Chemical Information and Modeling
- pH-Dependent Conformational Changes Lead to a Highly Shifted pKa for a Buried Glutamic Acid Mutant of SNase
- (2020) Ankita Sarkar et al. JOURNAL OF PHYSICAL CHEMISTRY B
- PKAD: a database of experimentally measured pKa values of ionizable groups in proteins
- (2019) Swagata Pahari et al. Database-The Journal of Biological Databases and Curation
- Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications
- (2019) Zhifeng Jing et al. Annual Review of Biophysics
- Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols
- (2019) Ernest Awoonor‐Williams et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- How Reactive are Druggable Cysteines in Protein Kinases?
- (2018) Ernest Awoonor-Williams et al. Journal of Chemical Information and Modeling
- The hydration structure of methylthiolate from QM/MM molecular dynamics
- (2018) Ernest Awoonor-Williams et al. JOURNAL OF CHEMICAL PHYSICS
- DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate
- (2018) Swagata Pahari et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology
- (2018) Matthias Gehringer et al. JOURNAL OF MEDICINAL CHEMISTRY
- Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems
- (2017) Brian K. Radak et al. Journal of Chemical Theory and Computation
- Targeted Covalent Inhibitors for Drug Design
- (2016) Thomas A. Baillie ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Cysteinome: The first comprehensive database for proteins with targetable cysteine and their covalent inhibitors
- (2016) Sijin Wu et al. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
- Covalent targeting of acquired cysteines in cancer
- (2016) Marieke Visscher et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Evaluation of Methods for the Calculation of the pKa of Cysteine Residues in Proteins
- (2016) Ernest Awoonor-Williams et al. Journal of Chemical Theory and Computation
- DelPhiPKa web server: predicting pKaof proteins, RNAs and DNAs
- (2015) Lin Wang et al. BIOINFORMATICS
- Covalent inhibitors in drug discovery: from accidental discoveries to avoided liabilities and designed therapies
- (2015) Renato A. Bauer DRUG DISCOVERY TODAY
- The basics of thiols and cysteines in redox biology and chemistry
- (2015) Leslie B. Poole FREE RADICAL BIOLOGY AND MEDICINE
- Polarizable force fields for molecular dynamics simulations of biomolecules
- (2015) Christopher M. Baker Wiley Interdisciplinary Reviews-Computational Molecular Science
- The pKa Value and Accessibility of Cysteine Residues Are Key Determinants for Protein Substrate Discrimination by Glutaredoxin
- (2014) Kristine Steen Jensen et al. BIOCHEMISTRY
- Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation
- (2014) Jason M. Swails et al. Journal of Chemical Theory and Computation
- Confidence limits, error bars and method comparison in molecular modeling. Part 1: The calculation of confidence intervals
- (2014) A. Nicholls JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Developing Irreversible Inhibitors of the Protein Kinase Cysteinome
- (2013) Qingsong Liu et al. CHEMISTRY & BIOLOGY
- Diverse Functional Roles of Reactive Cysteines
- (2012) Nicholas J. Pace et al. ACS Chemical Biology
- Understanding the pKa of Redox Cysteines: The Key Role of Hydrogen Bonding
- (2012) Goedele Roos et al. ANTIOXIDANTS & REDOX SIGNALING
- A Low pKaCysteine at the Active Site of Mouse Methionine Sulfoxide Reductase A
- (2012) Jung Chae Lim et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Factors Affecting Protein Thiol Reactivity and Specificity in Peroxide Reduction
- (2011) Gerardo Ferrer-Sueta et al. CHEMICAL RESEARCH IN TOXICOLOGY
- Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues
- (2011) Chresten R. Søndergaard et al. Journal of Chemical Theory and Computation
- PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions
- (2011) Mats H. M. Olsson et al. Journal of Chemical Theory and Computation
- Progress in the prediction of pKa values in proteins
- (2011) Emil Alexov et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- The pKa Cooperative: A collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins
- (2011) Jens E. Nielsen et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy
- (2011) Jason A. Wallace et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- LowModeMD—Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops
- (2010) Paul Labute Journal of Chemical Information and Modeling
- Predicting pKa
- (2009) Adam C. Lee et al. Journal of Chemical Information and Modeling
- MCCE2: Improving protein pKacalculations with extensive side chain rotamer sampling
- (2009) Yifan Song et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Cysteine pKaValues for the Bacterial Peroxiredoxin AhpC†‡
- (2008) Kimberly J. Nelson et al. BIOCHEMISTRY
- Cysteine pKaDepression by a Protonated Glutamic Acid in Human DJ-1†‡
- (2008) Anna C. Witt et al. BIOCHEMISTRY
- Benchmarking pKaPrediction Methods for Residues in Proteins
- (2008) Courtney L. Stanton et al. Journal of Chemical Theory and Computation
- Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures
- (2008) Paul Labute PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
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