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VISCANA: Visualized Cluster Analysis of Protein−Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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A parallelized integral-direct second-order M�ller?Plesset perturbation theory method with a fragment molecular orbital scheme
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Large scale MP2 calculations with fragment molecular orbital scheme
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Fragment molecular orbital method: application to polypeptides
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Fragment molecular orbital method: use of approximate electrostatic potential
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Fragment molecular orbital method: an approximate computational method for large molecules
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Pair interaction molecular orbital method: an approximate computational method for molecular interactions
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2-Amino-4,6-diarylpyridines as novel ligands for the estrogen receptor
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Consensus scoring for ligand/protein interactions
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Virtual screening—an overview
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Lead discovery using molecular docking
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Use of Structure−Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection
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Detailed Analysis of Scoring Functions for Virtual Screening
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Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
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Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein−Ligand Binding Interactions
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Fast prediction and visualization of protein binding pockets with PASS
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Molecular basis of agonism and antagonism in the oestrogen receptor
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Structure at 1.65 Å of RhoA and its GTPase-activating protein in complex with a transition-state analogue
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LIGAND: chemical database for enzyme reactions.
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KiBank: A Database for Computer-Aided Drug Design Based on Protein-Chemical Interaction Analysis
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Modeling and Visualization for the Fragment Molecular Orbital Method with the Graphical User Interface FU, and Analyses of Protein–Ligand Binding
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Quantum Mechanics in Structure‐Based Ligand Design
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Intra‐ and intermolecular interactions between cyclic‐AMP receptor protein and DNA: Ab initio fragment molecular orbital study
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FMO Drug Design Consortium
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Explicit solvation modulates intra- and inter-molecular interactions within DNA: Electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method
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Novel type of virtual ligand screening on the basis of quantum-chemical calculations for protein–ligand complexes and extended clustering techniques
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Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Møller-Plesset perturbation (MP2.5) scheme
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Application of singular value decomposition to the inter-fragment interaction energy analysis for ligand screening
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Fragment molecular orbital calculations on large scale systems containing heavy metal atom
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Fragment molecular orbital calculations on red fluorescent protein (DsRed)
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Large scale FMO-MP2 calculations on a massively parallel-vector computer
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An application of fragment interaction analysis based on local MP2
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Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)
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Fragment molecular orbital calculations for excitation energies of blue- and yellow-fluorescent proteins
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Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme
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Development of the four-body corrected fragment molecular orbital (FMO4) method
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Modeling of peptide–silica interaction based on four-body corrected fragment molecular orbital (FMO4) calculations
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Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method
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Proposal of novel potent inhibitors against androgen receptor based on ab initio molecular orbital calculations
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Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum simulation tool for large molecular systems
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Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods
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Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7)
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DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks
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BiRDS - Binding Residue Detection from Protein Sequences Using Deep ResNets
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Effect of Direct and Water-Mediated Interactions on the Identification of Hotspots in Biomolecular Complexes with Multiple Subsystems
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Protein–Ligand Empirical Interaction Components for Virtual Screening
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Dynamic Cooperativity of Ligand–Residue Interactions Evaluated with the Fragment Molecular Orbital Method
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Ab Initio Fragment Molecular Orbital Study of Molecular Interactions between Liganded Retinoid X Receptor and Its Coactivator; Part II: Influence of Mutations in Transcriptional Activation Function 2 Activating Domain Core on the Molecular Interactions
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GAMESS As a Free Quantum-Mechanical Platform for Drug Research
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Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD) Simulation
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Intermolecular Interaction Analyses on SARS-CoV-2 Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/peptide Using Fragment Molecular Orbital Calculation
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DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks
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A Mini-review on Chemoinformatics Approaches for Drug Discovery
inferred← citeshttps://doi.org/10.2751/jcac.20.1openalex-snapshot
A Radical Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA)
inferred← citeshttps://doi.org/10.3154/jvs.26.124openalex-snapshot
BioStation Viewer: Analysis and Visualization for Interactions of Bio-Macromolecules
inferred← citeshttps://doi.org/10.33774/chemrxiv-2021-013gnopenalex-snapshot
BiRDS - Binding Residue Detection from Protein Sequences using Deep ResNets
inferred← citeshttps://doi.org/10.33774/chemrxiv-2021-013gn-v2openalex-snapshot
BiRDS - Binding Residue Detection from Protein Sequences using Deep ResNets
inferred← citeshttps://doi.org/10.33774/chemrxiv-2021-7fkkx-v2openalex-snapshot
DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks
inferred← citeshttps://doi.org/10.3390/ijms161226202openalex-snapshot
Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods
inferred← citeshttps://doi.org/10.3390/ijms231911347openalex-snapshot
Interspecies Comparison of Interaction Energies between Photosynthetic Protein RuBisCO and 2CABP Ligand
inferred← citeshttps://doi.org/10.3390/molecules28248035openalex-snapshot
In Silico Design of Natural Inhibitors of ApoE4 from the Plant Moringa oleifera: Molecular Docking and Ab Initio Fragment Molecular Orbital Calculations
inferred← citeshttps://doi.org/10.35848/1347-4065/ac1857openalex-snapshot
Fragment molecular orbital based interaction analyses on complexes between SARS-CoV-2 RBD variants and ACE2
inferred← citeshttps://doi.org/10.35848/1347-4065/ade8c5openalex-snapshot
Prediction of quantitative interaction energy from low-cost FMO calculation by machine learning
inferred← citeshttps://doi.org/10.35848/1882-0786/abdac6openalex-snapshot
Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation
inferred← citeshttps://doi.org/10.4051/ibc.2010.2.2.0006openalex-snapshot
Fragment Molecular Orbital Method: Application to Protein-Ligand Binding
inferred← citeshttps://doi.org/10.6084/m9.figshare.26731063openalex-snapshot
Additional file 1 of PUResNetV2.0: a deep learning model leveraging sparse representation for improved ligand binding site prediction
inferred← citeshttps://doi.org/10.6084/m9.figshare.26731066openalex-snapshot
Additional file 2 of PUResNetV2.0: a deep learning model leveraging sparse representation for improved ligand binding site prediction
inferred← citeshttps://doi.org/10.7567/1347-4065/ab5335openalex-snapshot
Interaction between calcite and adsorptive peptide analyzed by fragment molecular orbital method
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