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Molecular Basis of Inactive B-RAFWT and B-RAFV600E Ligand Inhibition, Selectivity and Conformational Stability: An in Silico Study
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
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Development and testing of a general amber force field
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Scalable molecular dynamics with NAMD
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Derivation of rules for comparative protein modeling from a database of protein structure alignments
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Comparative Protein Modelling by Satisfaction of Spatial Restraints
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Novel knowledge-based mean force potential at atomic level
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Molecular Modeling and Prediction of Bioactivity
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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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Definition of general topological equivalence in protein structures
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VMD: Visual molecular dynamics
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Calculation of inhibitor Ki and inhibitor type from the concentration of inhibitor for 50% inhibition for Michaelis-Menten enzymes
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Dual binding site inhibitors of B-RAF kinase
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A combination of 3D-QSAR, docking, local-binding energy (LBE) and GRID study of the species differences in the carcinogenicity of benzene derivatives chemicals
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Mechanism of Activation of the RAF-ERK Signaling Pathway by Oncogenic Mutations of B-RAF
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VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs
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Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
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3D-QSAR and Molecular Mechanics Study for the Differences in the Azole Activity against Yeastlike and Filamentous Fungi and Their Relation to P450DM Inhibition. 1. 3-Substituted-4(3H)-quinazolinones
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The missing term in effective pair potentials
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Analysis of Binding Affinities for Celecoxib Analogues with COX-1 and COX-2 from Combined Docking and Monte Carlo Simulations and Insight into the COX-2/COX-1 Selectivity
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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
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Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model
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Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA
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A Computational Investigation of Allostery in the Catabolite Activator Protein
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Rapid and Accurate Prediction of Binding Free Energies for Saquinavir-Bound HIV-1 Proteases
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Comparative Binding Energy (COMBINE) Analysis of Influenza Neuraminidase−Inhibitor Complexes
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Novel Inhibitors of B-RAF Based on a Disubstituted Pyrazine Scaffold. Generation of a Nanomolar Lead
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MolDock: A New Technique for High-Accuracy Molecular Docking
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Molecular Recognition of Protein Kinase Binding Pockets for Design of Potent and Selective Kinase Inhibitors
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Comparative binding energy analysis
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Mutations of the BRAF gene in human cancer
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Switching on kinases: oncogenic activation of BRAF and the PDGFR family
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Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site
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Biochemical and molecular characterization of the novel BRAFV599Ins mutation detected in a classic papillary thyroid carcinoma
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Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer
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BRAFE600 in benign and malignant human tumours
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The selectivity of protein kinase inhibitors: a further update
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Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
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V600E B-Raf requires the Hsp90 chaperone for stability and is degraded in response to Hsp90 inhibitors
inferredcites →https://doi.org/10.1073/pnas.0711741105openalex-snapshot
Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity
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Toxicity study of allelochemical-like pesticides by a combination of 3D-QSAR, docking, Local Binding Energy (LBE) and GRID approaches
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Activation of B‐Raf kinase requires phosphorylation of the conserved residues Thr598 and Ser601
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The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification 1
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Structural Mechanism for STI-571 Inhibition of Abelson Tyrosine Kinase
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Comparative Protein Structure Modeling of Genes and Genomes
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Demonstration of a Genetic Therapeutic Index for Tumors Expressing Oncogenic BRAF by the Kinase Inhibitor SB-590885
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Akt3 and Mutant V600EB-Raf Cooperate to Promote Early Melanoma Development
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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How to obtain statistically converged MM/GBSA results
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Molecular mechanism of HIV‐1 integrase–vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective
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Computational algorithms for in silico profiling of activating mutations in cancer
inferred← citeshttps://doi.org/10.1016/j.jmgm.2009.12.005openalex-snapshot
The phosphorylation specificity of B-RAFWT, B-RAFD594V, B-RAFV600E and B-RAFK601E kinases: An in silico study
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Computational Study on the Interaction of N1 Substituted Pyrazole Derivatives with B-Raf Kinase: An Unusual Water Wire Hydrogen-Bond Network and Novel Interactions at the Entrance of the Active Site
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Molecular Dynamics Simulation, Free Energy Calculation and Structure-Based 3D-QSAR Studies of B-RAF Kinase Inhibitors
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Investigation of the Differences in Activity between Hydroxycycloalkyl N1 Substituted Pyrazole Derivatives As Inhibitors of B-Raf Kinase by Using Docking, Molecular Dynamics, QM/MM, and Fragment-BasedDe NovoDesign: Study of Binding Mode of Diastereomer Compounds
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Ligand Affinities Estimated by Quantum Chemical Calculations
inferred← citeshttps://doi.org/10.1021/jacs.5b01421openalex-snapshot
The Effect of a Widespread Cancer-Causing Mutation on the Inactive to Active Dynamics of the B-Raf Kinase
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Molecular Simulation Study of the Effect of Various Additives on Salbutamol Sulfate Crystal Habit
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Molecular Basis of the Interaction for an Essential Subunit PA−PB1 in Influenza Virus RNA Polymerase: Insights from Molecular Dynamics Simulation and Free Energy Calculation
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Computational studies of anaplastic lymphoma kinase mutations reveal common mechanisms of oncogenic activation
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Insight into the Structural Features of Pyrazolopyrimidine‐ and Pyrazolopyridine‐based B‐RafV600E Kinase Inhibitors by Computational Explorations
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Revealing selection in cancer using the predicted functional impact of cancer mutations. Application to nomination of cancer drivers
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An in silico study of the molecular basis of B-RAF activation and conformational stability
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