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Macrocycle Conformational Sampling with MacroModel

https://doi.org/10.1021/ci5001696
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What this work says

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

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Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
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Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
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Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94
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Merck molecular force field. IV. conformational energies and geometries for MMFF94
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Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules
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Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
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Fast, approximate algorithm for detection of solvent-inaccessible atoms
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Optimization of Gaussian surface calculations and extension to solvent-accessible surface areas
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MMFF VI. MMFF94s option for energy minimization studies
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MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries
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Low-mode conformational search elucidated: Application to C39H80 and flexible docking of 9-deazaguanine inhibitors into PNP
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Approximate solvent-accessible surface areas from tetrahedrally directed neighbor densities
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Hessian-free low-mode conformational search for large-scale protein loop optimization: application to c-jun N-terminal kinase JNK3
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A hierarchical approach to all‐atom protein loop prediction
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Epik: a software program for pK a prediction and protonation state generation for drug-like molecules
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Conformational changes of small molecules binding to proteins
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Towards the discovery of drug-like RNA ligands?
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Essential considerations for using protein–ligand structures in drug discovery
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A New Generation of Crystallographic Validation Tools for the Protein Data Bank
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The odyssey of marine pharmaceuticals: a current pipeline perspective
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A comparison of the Low Mode and Monte Carlo conformational search methods
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BIG HOPES RIDE ON BIG RINGS
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Comparative Analysis of Protein-Bound Ligand Conformations with Respect to Catalyst's Conformational Space Subsampling Algorithms
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ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers
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Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst
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Testing Physical Models of Passive Membrane Permeation
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PDB Ligand Conformational Energies Calculated Quantum-Mechanically
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Conformational Sampling of Bioactive Molecules: A Comparative Study
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Assessment of Conformational Ensemble Sizes Necessary for Specific Resolutions of Coverage of Conformational Space
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Torsion Angle Preference and Energetics of Small-Molecule Ligands Bound to Proteins
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Conformational Sampling of Druglike Molecules with MOE and Catalyst: Implications for Pharmacophore Modeling and Virtual Screening
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Conformational Analysis of Macrocycles: Finding What Common Search Methods Miss
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LowModeMD—Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops
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Ring Perception Using Breadth-First Search
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Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field
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Conformations of cycloheptadecane. A comparison of methods for conformational searching
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Semianalytical treatment of solvation for molecular mechanics and dynamics
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An internal-coordinate Monte Carlo method for searching conformational space
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Fully Flexible Low-Mode Docking: Application to Induced Fit in HIV Integrase
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Testing the Conformational Hypothesis of Passive Membrane Permeability Using Synthetic Cyclic Peptide Diastereomers
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Conformational Flexibility, Internal Hydrogen Bonding, and Passive Membrane Permeability: Successful in Silico Prediction of the Relative Permeabilities of Cyclic Peptides
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Low Mode Search. An Efficient, Automated Computational Method for Conformational Analysis: Application to Cyclic and Acyclic Alkanes and Cyclic Peptides
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Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding
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Intramolecular Hydrogen Bonding in Medicinal Chemistry
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Predicting and Improving the Membrane Permeability of Peptidic Small Molecules
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The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii
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Complex synthesis yields breast-cancer therapy
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Magic bullets in nature's arsenal
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The exploration of macrocycles for drug discovery — an underexploited structural class
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The Protein Data Bank
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The Cambridge Structural Database: a quarter of a million crystal structures and rising
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Implementing an X-ray validation pipeline for the Protein Data Bank
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Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination
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Probing the α‐Helical Structural Stability of Stapled p53 Peptides: Molecular Dynamics Simulations and Analysis
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Advances in the Development of Macrocyclic Inhibitors of Hepatitis C Virus NS3-4A Protease
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Chemoinformatic Analysis of Biologically Active Macrocycles
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Macrocyclic Inhibitors of Hsp90
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Editorial [Hot topic: Macrocycles in Medicinal Chemistry and Drug Discovery (Guest Editors: Adegboyega K. Oyelere)]

What points at this work

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

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Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00885openalex-snapshot
Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b01074openalex-snapshot
Toward Accurate Conformational Energies of Smaller Peptides and Medium-Sized Macrocycles: MPCONF196 Benchmark Energy Data Set
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00557openalex-snapshot
Docking Flexible Cyclic Peptides with AutoDock CrankPep
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.0c01500openalex-snapshot
Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.0c01505openalex-snapshot
Design of Thioether Cyclic Peptide Scaffolds with Passive Permeability and Oral Exposure
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.4c00204openalex-snapshot
Fast Quantitative Validation of 3D Models of Low-Affinity Protein–Ligand Complexes by STD NMR Spectroscopy
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.4c01555openalex-snapshot
Inhibition of Pseudomonas aeruginosa Carbonic Anhydrases, Exploring Ciprofloxacin Functionalization Toward New Antibacterial Agents: An In-Depth Multidisciplinary Study
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.4c02492openalex-snapshot
Impact of Linker Composition on VHL PROTAC Cell Permeability
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b01286openalex-snapshot
How Beyond Rule of 5 Drugs and Clinical Candidates Bind to Their Targets
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5c01540openalex-snapshot
Development of Next Generation Cell-Permeable Peptide Inhibitors for the Oncological Target MAGE-A4
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b00244openalex-snapshot
Atropisomer Control in Macrocyclic Factor VIIa Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b01329openalex-snapshot
Discovery of Potent Cyclophilin Inhibitors Based on the Structural Simplification of Sanglifehrin A
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6c01458openalex-snapshot
Identification of a New, Potent, and Stable Tetrahydroquinoline-Based 5-LOX/sEH Dual Inhibitor with Polymodal Anti-Inflammatory Activity in Acute Pancreatitis
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6c01558openalex-snapshot
Solution Ensembles of Griselimycin Expand the Definition of Molecular Chameleonicity
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.7b00359openalex-snapshot
Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.8b00347openalex-snapshot
Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.8b01292openalex-snapshot
qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps
inferred← citeshttps://doi.org/10.1021/acs.joc.2c00066openalex-snapshot
Comparing the Performances of Force Fields in Conformational Searching of Hydrogen-Bond-Donating Catalysts
inferred← citeshttps://doi.org/10.1021/acs.joc.4c00879openalex-snapshot
Influence of Selective Deoxyfluorination on the Molecular Structure of Type-2 N-Acetyllactosamine
inferred← citeshttps://doi.org/10.1021/acs.joc.5b02288openalex-snapshot
Distortion, Tether, and Entropy Effects on Transannular Diels–Alder Cycloaddition Reactions of 10–18-Membered Rings
inferred← citeshttps://doi.org/10.1021/acs.joc.6c01487openalex-snapshot
Gas-Phase Reactivity of Naphthalene-Based Singlet Oxenium Cations
inferred← citeshttps://doi.org/10.1021/acs.joc.7b01577openalex-snapshot
Model for the Enantioselectivity of Asymmetric Intramolecular Alkylations by Bis-Quaternized Cinchona Alkaloid-Derived Catalysts
inferred← citeshttps://doi.org/10.1021/acs.joc.9b01956openalex-snapshot
Synthesis of Forsythenethoside A, a Neuroprotective Macrocyclic Phenylethanoid Glycoside, and NMR Analysis of Conformers
inferred← citeshttps://doi.org/10.1021/acs.joc.9b03446openalex-snapshot
Catalytic Effects of Ammonium and Sulfonium Salts and External Electric Fields on Aza-Diels–Alder Reactions
inferred← citeshttps://doi.org/10.1021/acs.jpca.1c01294openalex-snapshot
Exploring Avenues beyond Revised DSD Functionals: I. Range Separation, with xDSD as a Special Case
inferred← citeshttps://doi.org/10.1021/acs.jpca.3c02360openalex-snapshot
Theoretical Insights into the Ultrafast Deactivation Mechanism and Photostability of a Natural Sunscreen System: Mycosporine Glycine
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c01669openalex-snapshot
Evaluating the Conformations and Dynamics of Peptoid Macrocycles
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c05470openalex-snapshot
Ensemble Generation for Linear and Cyclic Peptides Using a Reservoir Replica Exchange Molecular Dynamics Implementation in GROMACS
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6c00660openalex-snapshot
Ensemble Sensitivity to Chemical Modifications in Free and Bound Macrocyclic Peptides
inferred← citeshttps://doi.org/10.1021/acs.orglett.7b02851openalex-snapshot
Origins of Stereoselectivity in Chiral Aminoalcohol Catalysis of Oxyallyl Cation–Indole Reactions
inferred← citeshttps://doi.org/10.1021/acschemneuro.5c00201openalex-snapshot
Mathematical Modeling of Aβ-42 Dimerization Dynamics: Integrating Physics-Based Simulations, Graph-Based Variational Autoencoder-Driven Neural Relational Inference, and Chaos Theory
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.1c00251openalex-snapshot
The Growing Importance of Chirality in 3D Chemical Space Exploration and Modern Drug Discovery Approaches for Hit-ID
inferred← citeshttps://doi.org/10.1021/acsomega.4c04023openalex-snapshot
Rational Design Problematics of Peptide Nucleic Acids as SARS-CoV-2 Inhibitors
inferred← citeshttps://doi.org/10.1021/acsomega.4c09944openalex-snapshot
3,3′-Diindolylmethane (DIM): A Molecular Scaffold for Inhibition of WWP1 and WWP2, Members of the NEDD4 Family HECT E3 Ligases
inferred← citeshttps://doi.org/10.1021/acsomega.6c03194openalex-snapshot
Anti-Inflammatory Activity of Monoterpene Phenol Dimers from Satureja bachtiarica
inferred← citeshttps://doi.org/10.1021/acsomega.8b01379openalex-snapshot
Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?
inferred← citeshttps://doi.org/10.1021/acsomega.9b03525openalex-snapshot
Synthesis and Characterization of a Click-Assembled 18-Atom Macrocycle That Displays Selective AXL Kinase Inhibitory Activity
inferred← citeshttps://doi.org/10.1021/acsomega.9b03797openalex-snapshot
Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study
inferred← citeshttps://doi.org/10.1021/bk-2022-1417.ch003openalex-snapshot
Computational Design of Peptide-Based Binders to Therapeutic Targets
inferred← citeshttps://doi.org/10.1021/bk-2022-1417.ch004openalex-snapshot
Roles of Conformations on Predictions of Peptide Properties
inferred← citeshttps://doi.org/10.1021/bk-2022-1417.ch005openalex-snapshot
Matching Simulations and Experiments of Conformationally Flexible Cyclic Peptides: Steps toward a Holistic View of Passive Membrane Permeability
inferred← citeshttps://doi.org/10.1021/bk-2022-1417.ch006openalex-snapshot
NMR Spectroscopy for Studying Peptide Conformations and Cell Permeability
inferred← citeshttps://doi.org/10.1021/bk-2022-1417.ch008openalex-snapshot
Design and Discovery of Orally Bioavailable Macrocycles: Toward Orally Bioavailable Peptide Therapeutics
inferred← citeshttps://doi.org/10.1021/jacs.0c09310openalex-snapshot
Photorearrangement of [8]-2,6-Pyridinophane N-Oxide
inferred← citeshttps://doi.org/10.1021/jacs.0c12329openalex-snapshot
A Hexapodal Capsule for the Recognition of Anions
inferred← citeshttps://doi.org/10.1021/jacs.4c13485openalex-snapshot
Mechanistic Interrogation of Photochemical Nickel-Catalyzed Tetrahydrofuran Arylation Leveraging Enantioinduction Data
inferred← citeshttps://doi.org/10.1021/jacs.6b00712openalex-snapshot
Flexibility Coexists with Shape-Persistence in Cyanostar Macrocycles
inferred← citeshttps://doi.org/10.1021/jacs.6b13243openalex-snapshot
Quantifying Possible Routes for SpnF-Catalyzed Formal Diels–Alder Cycloaddition
inferred← citeshttps://doi.org/10.1021/jacsau.4c01140openalex-snapshot
STD NMR Epitope Perturbation by Mutation Unveils the Mechanism of YM155 as an Arginine-Glycosyltransferases Inhibitor Effective in Treating Enteropathogenic Diseases
inferred← citeshttps://doi.org/10.1038/s41467-024-49891-wopenalex-snapshot
Widespread exposure to SARS-CoV-2 in wildlife communities
inferred← citeshttps://doi.org/10.1038/s41557-025-01738-7openalex-snapshot
Discovery of a fluorinated macrobicyclic antibiotic through chemical synthesis
inferred← citeshttps://doi.org/10.1038/s41597-024-03698-yopenalex-snapshot
CREMP: Conformer-rotamer ensembles of macrocyclic peptides for machine learning
inferred← citeshttps://doi.org/10.1038/s41598-018-24766-5openalex-snapshot
High throughput evaluation of macrocyclization strategies for conformer stabilization
inferred← citeshttps://doi.org/10.1038/s41598-023-29996-wopenalex-snapshot
Sunsetting Binding MOAD with its last data update and the addition of 3D-ligand polypharmacology tools
inferred← citeshttps://doi.org/10.1039/c7ob01448aopenalex-snapshot
Chemical optimization of macrocyclic HIV-1 inactivators for improving potency and increasing the structural diversity at the triazole ring
inferred← citeshttps://doi.org/10.1039/c9cp06869dopenalex-snapshot
Automated exploration of the low-energy chemical space with fast quantum chemical methods
inferred← citeshttps://doi.org/10.1039/d1md00098eopenalex-snapshot
Cyclisation strategies for stabilising peptides with irregular conformations
inferred← citeshttps://doi.org/10.1039/d2cb00016dopenalex-snapshot
Navigating complex peptide structures using macrocycle conformational maps
inferred← citeshttps://doi.org/10.1039/d3dd00053bopenalex-snapshot
MacroConf – dataset & workflows to assess cyclic peptide solution structures
inferred← citeshttps://doi.org/10.1039/d4dt00902aopenalex-snapshot
Coordinating nature of M 6 L 12 double-stranded macrocycles: co-ligand competition of perchlorate, water, and acetonitrile depending on metal( ii ) ions
inferred← citeshttps://doi.org/10.1039/d5re00402kopenalex-snapshot
On the automated determination of p K a by NMR in DMSO : water mixtures
inferred← citeshttps://doi.org/10.1039/d6cs00079gopenalex-snapshot
An overview of reaction outcome prediction with physics-based and data-driven methods
inferred← citeshttps://doi.org/10.1055/a-2486-9139openalex-snapshot
New Constituents from Zanthoxylum rhoifolium
inferred← citeshttps://doi.org/10.1055/s-0036-1591975openalex-snapshot
Artificial Macrocycles
inferred← citeshttps://doi.org/10.1063/5.0213317openalex-snapshot
Quantum chemical package Jaguar: A survey of recent developments and unique features
inferred← citeshttps://doi.org/10.1063/5.0320687openalex-snapshot
The role of ring puckering and non-covalent interactions in the conformational chirality of 2,5-diketopiperazines with identical residues: A theoretical study
inferred← citeshttps://doi.org/10.1101/2022.09.07.507010openalex-snapshot
Accelerated ensemble generation for cyclic peptides using a Reservoir-REMD implementation in GROMACS
inferred← citeshttps://doi.org/10.1101/2025.03.10.642353openalex-snapshot
Deciphering the role of histo-blood group antigens in bovine rotavirus C infection
inferred← citeshttps://doi.org/10.1101/2025.03.18.643899openalex-snapshot
Directed Chemical Evolution via Navigating Molecular Encoding Space
inferred← citeshttps://doi.org/10.1101/2025.07.04.663252openalex-snapshot
Discovery of Niclosamide Analogs with Potent Mitochondrial Uncoupling Activity with reduced toxicity
inferred← citeshttps://doi.org/10.1111/bph.70626openalex-snapshot
Chemoproteomic discovery of a brain‐penetrant, covalent NLRP3 inhibitor that binds a novel allosteric pocket
inferred← citeshttps://doi.org/10.1111/mmi.15380openalex-snapshot
The Flagellin‐Specific Chaperone FliS of Borrelia burgdorferi Controls the Cytoplasmic Pool of Flagellins at the Level of Translation Initiation, Secretion, and Proteolysis
inferred← citeshttps://doi.org/10.1124/mol.118.114082openalex-snapshot
Molecular Basis of Action of a Small-Molecule Positive Allosteric Modulator Agonist at the Type 1 Cholecystokinin Holoreceptor
inferred← citeshttps://doi.org/10.1142/s2737416525501261openalex-snapshot
Integrated Virtual Screening of Anthraquinone Derivatives for Anticancer Drug Discovery
inferred← citeshttps://doi.org/10.1177/17475198241305254openalex-snapshot
A density functional theory study of keto-enol tautomerism in 1,2-cyclodiones: Substituent effects on reactivity and thermodynamic stability
inferred← citeshttps://doi.org/10.1186/s13321-017-0216-0openalex-snapshot
Searching for bioactive conformations of drug-like ligands with current force fields: how good are we?
inferred← citeshttps://doi.org/10.1515/chem-2023-0161openalex-snapshot
Utilization of computational methods for the identification of new natural inhibitors of human neutrophil elastase in inflammation therapy
inferred← citeshttps://doi.org/10.21203/rs.3.rs-1597257/v1openalex-snapshot
High-Quality Conformer Generation with CDPKit/CONFORT: Algorithm and Performance Assessment
inferred← citeshttps://doi.org/10.2210/pdb6dmj/pdbopenalex-snapshot
A multiconformer ligand model of inhibitor 53W bound to CREB binding protein bromodomain
inferred← citeshttps://doi.org/10.2298/jsc251104018aopenalex-snapshot
Syntheses and computational analyses of selected macrolide derivatives derived from clarithromycin A
inferred← citeshttps://doi.org/10.33612/diss.193912062openalex-snapshot
In Silico Design and Selection of CD44 Antagonists
inferred← citeshttps://doi.org/10.3389/fmicb.2025.1662803openalex-snapshot
The extracellular domain of SaNSrFP binds bacitracin and allows the identification of new members of the BceAB transporter family
inferred← citeshttps://doi.org/10.3390/biom9110745openalex-snapshot
Molecular Dynamics Simulations Suggest a Non-Doublet Decoding Model of −1 Frameshifting by tRNASer3
inferred← citeshttps://doi.org/10.3390/genes11080941openalex-snapshot
The Role of APOSTART in Switching between Sexuality and Apomixis in Poa pratensis
inferred← citeshttps://doi.org/10.3390/ijms20205152openalex-snapshot
Chemical Modification of Microcin J25 Reveals New Insights on the Stereospecific Requirements for Antimicrobial Activity
inferred← citeshttps://doi.org/10.3390/ijms26031285openalex-snapshot
Rational Identification of Ritonavir as IL-20 Receptor A Ligand Endowed with Antiproliferative Properties in Breast Cancer Cells
inferred← citeshttps://doi.org/10.3390/ijms26199606openalex-snapshot
Vincristine Beyond Mitosis: Uncovering a First Link to G-Quadruplex DNA in Cancer Cells
inferred← citeshttps://doi.org/10.3390/ijms262010239openalex-snapshot
Discovery of N-Hydroxypyridinedione-Based Inhibitors of HBV RNase H: Design, Synthesis, and Extended SAR Studies
inferred← citeshttps://doi.org/10.3390/ijms262412038openalex-snapshot
In Silico Lead Identification of Staphylococcus aureus LtaS Inhibitors: A High-Throughput Computational Pipeline Towards Prototype Development
inferred← citeshttps://doi.org/10.3390/molecules201018732openalex-snapshot
Charting a Path to Success in Virtual Screening
inferred← citeshttps://doi.org/10.3390/molecules22010136openalex-snapshot
The Performance of Several Docking Programs at Reproducing Protein–Macrolide-Like Crystal Structures
inferred← citeshttps://doi.org/10.3390/molecules30234636openalex-snapshot
Discovery of Influenza Neuraminidase Inhibitors: Structure-Based Virtual Screening and Biological Evaluation of Novel Chemotypes
inferred← citeshttps://doi.org/10.3390/ph18020174openalex-snapshot
Repurposing FDA-Approved Agents to Develop a Prototype Helicobacter pylori Shikimate Kinase (HPSK) Inhibitor: A Computational Approach Using Virtual Screening, MM-GBSA Calculations, MD Simulations, and DFT Analysis
inferred← citeshttps://doi.org/10.3390/sym16121668openalex-snapshot
Favorable Symmetric Structures of Radiopharmaceutically Important Neutral Cyclen-Based Ligands
inferred← citeshttps://doi.org/10.3390/sym17091466openalex-snapshot
Favorable Symmetric Structures of Radiopharmaceutically Important Anionic (2-) Cyclen-Based Ligands
inferred← citeshttps://doi.org/10.4155/fmc-2018-0400openalex-snapshot
Energy Windows for Computed Compound Conformers: Covering Artefacts Or Truly Large Reorganization Energies?
inferred← citeshttps://doi.org/10.48550/arxiv.2305.08057openalex-snapshot
CREMP: Conformer-rotamer ensembles of macrocyclic peptides for machine learning
inferred← citeshttps://doi.org/10.5334/jors.189openalex-snapshot
ConfBuster: Open-Source Tools for Macrocycle Conformational Search and Analysis
inferred← citeshttps://doi.org/10.7554/elife.52978openalex-snapshot
C-mannosylation supports folding and enhances stability of thrombospondin repeats
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