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Conformational Analysis of Macrocycles: Finding What Common Search Methods Miss

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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. 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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Efficient algorithm for conformational search of macrocyclic molecules

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Strain-Induced “Band Flips” in Cyclodecaamylose and Higher Homologues

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Molecular Catenanes, Rotaxanes and Knots

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Supramolecular Chemistry—Scope and Perspectives Molecules, Supermolecules, and Molecular Devices (Nobel Lecture)

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Perspectives in Supramolecular Chemistry—From Molecular Recognition towards Molecular Information Processing and Self‐Organization

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NMR Spectroscopy Techniques for Screening and Identifying Ligand Binding to Protein Receptors

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Geldanamycin, an inhibitor of the chaperone activity of HSP90, induces MAPK‐independent cell cycle arrest

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Parameterization of OPLS–AA force field for the conformational analysis of macrocyclic polyketides

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Efficient exploration of conformational space using the stochastic search method: application to β‐peptide oligomers

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A distance geometry heuristic for expanding the range of geometries sampled during conformational search

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Self‐organizing superimposition algorithm for conformational sampling

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An efficient newton‐like method for molecular mechanics energy minimization of large molecules

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Stochastic search for the conformations of bicyclic hydrocarbons

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Improvements to the distance geometry algorithm for conformational sampling of cyclic structures

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Conformational searching methods for small molecules. II. Genetic algorithm approach

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Poling: Promoting conformational variation

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Pharmacophore‐based molecular docking to account for ligand flexibility

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High-resolution structure of a potent, cyclic proteinase inhibitor from sunflower seeds

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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

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Conformational states and biological activity of cyclic peptides

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Synthesis, solution structure, and bioactivity of six new simplified analogues of the natural cyclodepsipeptide jaspamide

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TOR Signaling in Growth and Metabolism

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Structural and Antitumor Properties of the YSNSG Cyclopeptide Derived from Tumstatin

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Clinical efficacy of new antifungal agents

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An orthorhombic crystal form of cyclohexaicosaose, CA26·32.59 H2O: comparison with the triclinic form

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Conformation of cyclomaltooligosaccharide (“cycloamylose”) of dp21 in aqueous solution

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Cylindramide: Cytotoxic tetramic acid lactam from the marine sponge Halichondria cylindrata Tanita & Hoshino

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Polyoxypeptin isolated from Streptomyces: A bioactive cyclic depsipeptide containing the novel amino acid 3-hydroxy-3-methylproline

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Analysis and optimization of structure-based virtual screening protocols

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Empirical modifications to the Amber/OPLS potential for predicting the solution conformations of cyclic peptides by vacuum calculations

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A combined model-building and distance-geometry approach to automated conformational analysis and search

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Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures

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Conformational Sampling by Self-Organization

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Comparative Analysis of Protein-Bound Ligand Conformations with Respect to Catalyst's Conformational Space Subsampling Algorithms

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MIMUMBA Revisited: Torsion Angle Rules for Conformer Generation Derived from X-ray Structures

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Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations

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Conformational Sampling of Bioactive Molecules: A Comparative Study

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CAESAR: A New Conformer Generation Algorithm Based on Recursive Buildup and Local Rotational Symmetry Consideration

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Advanced Biological and Chemical Discovery (ABCD): Centralizing Discovery Knowledge in an Inherently Decentralized World

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A new approach to probing conformational space with molecular mechanics: random incremental pulse search

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An internal-coordinate Monte Carlo method for searching conformational space

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Halipeptins A and B: Two Novel Potent Anti-inflammatory Cyclic Depsipeptides from the Vanuatu Marine Sponge Haliclona species

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Cyclic RGD Peptides Containing β-Turn Mimetics

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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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Insights into the Structure of Large-Ring Cyclodextrins through Molecular Dynamics Simulations in Solution

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Two Novel Cyclic Peptides with Antifungal Activity from the Cyanobacterium Tolypothrix byssoidea (EAWAG 195)

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Conformational analysis of six- and twelve-membered ring compounds by molecular dynamics

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Large Cyclodextrins

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The exploration of macrocycles for drug discovery — an underexploited structural class

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Combinatorial informatics in the post-genomics era

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Marine metabolites and metal ion chelation. Circular dichroism studies of metal binding to Lissoclinum cyclopeptides

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V-Amylose at atomic resolution: X-ray structure of a cycloamylose with 26 glucose residues (cyclomaltohexaicosaose)

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Stable calculation of coordinates from distance information

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On the Effects of Permuted Input on Conformational Sampling of Drug‐like Molecules: an Evaluation of Stochastic Proximity Embedding

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Antimitotic Activity of the Potent Tumor Inhibitor Maytansine

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Optimization by Simulated Annealing

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The Discovery of Crown Ethers

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High-Temperature Simulation of Dynamics of Cyclohexane.

What points at this work

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

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Cheminformatics

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Macrocycles as Templates for Diversity Generation in Drug Discovery

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Contemporary Macrocyclization Technologies

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Dynamics of the Glycosidic Bond: Conformational Space of Lactose

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Is conformational sampling of drug‐like molecules a solved problem?

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Stochastic Proximity Embedding: Methods and Applications

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VSPrep: A General KNIME Workflow for the Preparation of Molecules for Virtual Screening

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Stochastic Proximity Embedding: A Simple, Fast and Scalable Algorithm for Solving the Distance Geometry Problem

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Application of shape-based and pharmacophore-based in silico screens for identification of Type II protein kinase inhibitors

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Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen

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D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

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Design and applications of cyclic peptides

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Current Trends in Macrocyclic Drug Discovery and beyond -Ro5

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Tackling the conformational sampling of larger flexible compounds and macrocycles in pharmacology and drug discovery

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Modelling the binding mode of macrocycles: Docking and conformational sampling

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Computational methods to design cyclic peptides

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Proline-mediated formation of novel chroman-4-one tetrahydropyrimidines

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Conformational Control of Macrocycles by Remote Structural Modification

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Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences

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Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments

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Decisions with Confidence: Application to the Conformation Sampling of Molecules in the Solid State

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Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock

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Simulation Reveals the Chameleonic Behavior of Macrocycles

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Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics

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Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction

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Docking of Macrocycles: Comparing Rigid and Flexible Docking in Glide

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Improving Accuracy, Diversity, and Speed with Prime Macrocycle Conformational Sampling

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Macrocycle Conformational Sampling by DFT-D3/COSMO-RS Methodology

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Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization

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Conformator: A Novel Method for the Generation of Conformer Ensembles

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Cyclization and Docking Protocol for Cyclic Peptide–Protein Modeling Using HADDOCK2.4

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Conformational Analysis of Macrocyclic Compounds Using a Machine-Learned Interatomic Potential

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Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics

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Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins

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Conformational Strain of Macrocyclic Peptides in Ligand–Receptor Complexes Based on Advanced Refinement of Bound-State Conformers

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Conformational Effects on the Passive Membrane Permeability of Synthetic Macrocycles

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Macrocycles in Drug Discovery─Learning from the Past for the Future

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Linker Modification Enables Control of Key Functional Group Orientation in Macrocycles

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Orally Bioavailable Cyclin A/B RxL Inhibitors: Optimization of a Novel Class of Macrocyclic Peptides That Target E2F-High and G1–S-Checkpoint-Compromised Cancers

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Accurate Physics-Based Flexible Docking of Macrocyclic Ligands

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Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors

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Free Ligand 1D NMR Conformational Signatures To Enhance Structure Based Drug Design of a Mcl-1 Inhibitor (AZD5991) and Other Synthetic Macrocycles

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Evaluating the Conformations and Dynamics of Peptoid Macrocycles

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Determining the Predominant Conformations of Mortiamides A–D in Solution Using NMR Data and Molecular Modeling Tools

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Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?

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Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study

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NMR Spectroscopy for Studying Peptide Conformations and Cell Permeability

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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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Stochastic Proximity Embedding on Graphics Processing Units: Taking Multidimensional Scaling to a New Scale

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Recognizing Pitfalls in Virtual Screening: A Critical Review

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Macrocycle Conformational Sampling with MacroModel

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Knowledge-Based Libraries for Predicting the Geometric Preferences of Druglike Molecules

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Conformational Sampling with Stochastic Proximity Embedding and Self-Organizing Superimposition: Establishing Reasonable Parameters for Their Practical Use

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LowModeMD—Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops

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Exploring the Energy Landscapes of Cyclic Tetrapeptides with Discrete Path Sampling

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Energy Landscapes and Global Optimization of Self-Assembling Cyclic Peptides

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Flexibility Coexists with Shape-Persistence in Cyanostar Macrocycles

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Computational and Experimental Investigations into the Conformations of Cyclic Tetra-α/β-peptides

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Macrocycles: lessons from the distant past, recent developments, and future directions

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Automated exploration of the low-energy chemical space with fast quantum chemical methods

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Selective host–guest chemistry, self-assembly and conformational preferences of m -xylene macrocycles probed by ion-mobility spectrometry mass spectrometry

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MacroConf – dataset & workflows to assess cyclic peptide solution structures

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Late-stage chirality generation strategies for the total synthesis of macrocyclic natural products

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A Cyclisation and Docking Protocol for Cyclic Peptide-Protein Modelling using HADDOCK2.4

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Open Source Software and Web Services for Designing Therapeutic Molecules

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Energy Windows for Computed Compound Conformers: Covering Artefacts Or Truly Large Reorganization Energies?

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ConfBuster: Open-Source Tools for Macrocycle Conformational Search and Analysis

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