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Analyses of Activity for Factor Xa Inhibitors Based on Monte Carlo Simulations

https://doi.org/10.1021/jm030288d
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Free energies of solvation in chloroform and water from a linear response approach
inferredcites →https://doi.org/10.1006/jmbi.1993.1441openalex-snapshot
Structure of Human Des(1-45) Factor Xa at 2·2 Å Resolution
inferredcites →https://doi.org/10.1007/bf00117280openalex-snapshot
Class IV charge models: A new semiempirical approach in quantum chemistry
inferredcites →https://doi.org/10.1007/s00018-002-8415-9openalex-snapshot
Visions & Reflections Factor Xa - a promising target for drug development
inferredcites →https://doi.org/10.1007/s0089490050141openalex-snapshot
Encyclopedia of Computational Chemistry
inferredcites →https://doi.org/10.1016/s0960-894x(01)00825-3openalex-snapshot
Estimation of Binding Affinities for Celecoxib Analogues with COX-2 via Monte Carlo-Extended Linear Response
inferredcites →https://doi.org/10.1016/s0960-894x(03)00681-4openalex-snapshot
Activity predictions for efavirenz analogues with the K103N mutant of HIV reverse transcriptase
inferredcites →https://doi.org/10.1021/ar00161a004openalex-snapshot
Free energy calculations: a breakthrough for modeling organic chemistry in solution
inferredcites →https://doi.org/10.1021/bi00107a001openalex-snapshot
The coagulation cascade: initiation, maintenance, and regulation
inferredcites →https://doi.org/10.1021/bi001477qopenalex-snapshot
Preparation, Characterization, and the Crystal Structure of the Inhibitor ZK-807834 (CI-1031) Complexed with Factor Xa,
inferredcites →https://doi.org/10.1021/cr00023a004openalex-snapshot
Free energy calculations: Applications to chemical and biochemical phenomena
inferredcites →https://doi.org/10.1021/j100026a034openalex-snapshot
An Extended Linear Response Method for Determining Free Energies of Hydration
inferredcites →https://doi.org/10.1021/ja003113ropenalex-snapshot
Validation of a Model for the Complex of HIV-1 Reverse Transcriptase with Sustiva through Computation of Resistance Profiles
inferredcites →https://doi.org/10.1021/ja034308copenalex-snapshot
Validation of a Model for the Complex of HIV-1 Reverse Transcriptase with Nonnucleoside Inhibitor TMC125
inferredcites →https://doi.org/10.1021/ja9621760openalex-snapshot
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
inferredcites →https://doi.org/10.1021/ja993663topenalex-snapshot
Prediction of Properties from Simulations: Free Energies of Solvation in Hexadecane, Octanol, and Water
inferredcites →https://doi.org/10.1021/jm000255nopenalex-snapshot
Estimation of Binding Affinities for HEPT and Nevirapine Analogues with HIV-1 Reverse Transcriptase via Monte Carlo Simulations
inferredcites →https://doi.org/10.1021/jm000405uopenalex-snapshot
Estimation of Binding Affinities for Selective Thrombin Inhibitors via Monte Carlo Simulations
inferredcites →https://doi.org/10.1021/jm0100638openalex-snapshot
Development of Serine Protease Inhibitors Displaying a Multicentered Short (<2.3 Å) Hydrogen Bond Binding Mode: Inhibitors of Urokinase-Type Plasminogen Activator and Factor Xa
inferredcites →https://doi.org/10.1021/jm010580qopenalex-snapshot
Prediction of Activity for Nonnucleoside Inhibitors with HIV-1 Reverse Transcriptase Based on Monte Carlo Simulations
inferredcites →https://doi.org/10.1021/jm0200660openalex-snapshot
Design, Synthesis, and Activity of a Novel Series of Factor Xa Inhibitors: Optimization of Arylamidine Groups
inferredcites →https://doi.org/10.1021/jm960728jopenalex-snapshot
Cyclic HIV-1 Protease Inhibitors Derived from Mannitol: Synthesis, Inhibitory Potencies, and Computational Predictions of Binding Affinities
inferredcites →https://doi.org/10.1021/jm990326mopenalex-snapshot
1,2-Dibenzamidobenzene Inhibitors of Human Factor Xa
inferredcites →https://doi.org/10.1023/a:1007930623000openalex-snapshot
Ligand binding affinity prediction by linear interaction energy methods
inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot
Comparison of simple potential functions for simulating liquid water
inferredcites →https://doi.org/10.1093/protein/7.3.385openalex-snapshot
A new method for predicting binding affinity in computer-aided drug design
inferredcites →https://doi.org/10.1093/protein/8.11.1137openalex-snapshot
Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations
inferredcites →https://doi.org/10.1093/protein/9.7.567openalex-snapshot
Binding free energy calculations for P450cam-substrate complexes
inferredcites →https://doi.org/10.3109/9781420069242openalex-snapshot
New Therapeutic Agents in Thrombosis and Thrombolysis

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Computation of Drug‐Binding Thermodynamics
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Free Energy Calculations: Approximate Methods for Biological Macromolecules
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Residue‑resolved dynamically averaged interaction analysis of direct factor Xa inhibitors by MD‑FMO combination calculations
inferred← citeshttps://doi.org/10.1007/s10910-005-9035-zopenalex-snapshot
An overlooked property of plot methods
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Synthesis, Docking, and Anticoagulant Activity of New Factor-Xa Inhibitors in a Series of Pyrrolo[3,2,1-ij]Quinoline-1,2-Diones
inferred← citeshttps://doi.org/10.1007/s11172-021-3114-6openalex-snapshot
Synthesis and study of new 2H-pyranoquinolin-2-one-based inhibitors of blood coagulation factors Xa and XIa
inferred← citeshttps://doi.org/10.1016/bs.aihch.2022.10.001openalex-snapshot
The chemistry of citrazinic acid (2,6-dihydroxyisonicotinic acid)
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Pharmacophore Identification, in Silico Screening, and Virtual Library Design for Inhibitors of the Human Factor Xa
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Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA
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A GRID-Derived Water Network Stabilizes Molecular Dynamics Computer Simulations of a Protease
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MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization
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“Adapted Linear Interaction Energy”: A Structure-Based LIE Parametrization for Fast Prediction of Protein–Ligand Affinities
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General Model for Estimation of the Inhibition of Protein Kinases Using Monte Carlo Simulations
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Applying Linear Interaction Energy Method for Rational Design of Noncompetitive Allosteric Inhibitors of the Sarco- and Endoplasmic Reticulum Calcium-ATPase
inferred← citeshttps://doi.org/10.1021/jp051105xopenalex-snapshot
Processing Multimode Binding Situations in Simulation-Based Prediction of Ligand−Macromolecule Affinities
inferred← citeshttps://doi.org/10.1021/jp101654gopenalex-snapshot
Stabilizing of a Globular Protein by a Highly Complex Water Network: A Molecular Dynamics Simulation Study on Factor Xa
inferred← citeshttps://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferred← citeshttps://doi.org/10.1080/00268970500298980openalex-snapshot
New mean-energy formulae for free energy differences
inferred← citeshttps://doi.org/10.1080/08927022.2012.741235openalex-snapshot
3D-QSAR, docking and molecular dynamics for factor Xa inhibitors as anticoagulant agents
inferred← citeshttps://doi.org/10.1080/08982104.2017.1381115openalex-snapshot
SPIN: rapid synthesis, purification, and concentration of small drug-loaded liposomes
inferred← citeshttps://doi.org/10.1080/10629360902949294openalex-snapshot
Application of the linear interaction energy method for rational design of artemisinin analogues as haeme polymerisation inhibitors
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The Many Roles of Computation in Drug Discovery
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Application of Molecular Modeling to Development of New Factor Xa Inhibitors
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