Conformational analysis of macrocycles: comparing general and specialized methods

Conformator: A Novel Method for the Generation of Conformer Ensembles

(2019) Nils-Ole Friedrich et al.   Journal of Chemical Information and Modeling

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

(2017) Ondrej Gutten et al.   Journal of Chemical Information and Modeling

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

(2017) Dan Sindhikara et al.   Journal of Chemical Information and Modeling

Docking of Macrocycles: Comparing Rigid and Flexible Docking in Glide

(2017) Hiba Alogheli et al.   Journal of Chemical Information and Modeling

Conformation Generation: The State of the Art

(2017) Paul C. D. Hawkins   Journal of Chemical Information and Modeling

ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs

(2017) Ann E. Cleves et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding

(2017) Megan L. Peach et al.   JOURNAL OF MOLECULAR RECOGNITION

Towards understanding the unbound state of drug compounds: Implications for the intramolecular reorganization energy upon binding

(2016) Nicolas Foloppe et al.   BIOORGANIC & MEDICINAL CHEMISTRY

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

(2016) Qin Wang et al.   Journal of Chemical Information and Modeling

Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics

(2016) Evangelos A. Coutsias et al.   Journal of Chemical Theory and Computation

Targeting protein−protein interfaces using macrocyclic peptides

(2015) Meng Gao et al.   BIOPOLYMERS

Toward Focusing Conformational Ensembles on Bioactive Conformations: A Molecular Mechanics/Quantum Mechanics Study

(2015) Hannah H. Avgy-David et al.   Journal of Chemical Information and Modeling

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

Models of protein–ligand crystal structures: trust, but verify

(2015) Marc C. Deller et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

How Beyond Rule of 5 Drugs and Clinical Candidates Bind to Their Targets

(2015) Bradley C. Doak et al.   JOURNAL OF MEDICINAL CHEMISTRY

Macrocycle Conformational Sampling with MacroModel

(2014) K. Shawn Watts et al.   Journal of Chemical Information and Modeling

Comprehensive analysis of loops at protein-protein interfaces for macrocycle design

(2014) Jason Gavenonis et al.   Nature Chemical Biology

How proteins bind macrocycles

(2014) Elizabeth A Villar et al.   Nature Chemical Biology

Quantification of free ligand conformational preferences by NMR and their relationship to the bioactive conformation

(2013) Charles D. Blundell et al.   BIOORGANIC & MEDICINAL CHEMISTRY

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

(2013) I-Jen Chen et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

(2013) G. Madhavi Sastry et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Macrocyclic Drugs and Clinical Candidates: What Can Medicinal Chemists Learn from Their Properties?

(2013) Fabrizio Giordanetto et al.   JOURNAL OF MEDICINAL CHEMISTRY

Macrocyclic Drugs and Synthetic Methodologies toward Macrocycles

(2013) Xufen Yu et al.   MOLECULES

A strategy for the diversity-oriented synthesis of macrocyclic scaffolds using multidimensional coupling

(2013) Henning S. G. Beckmann et al.   Nature Chemistry

Macrocycles in new drug discovery

(2012) Jamie Mallinson et al.   Future Medicinal Chemistry

PDB Ligand Conformational Energies Calculated Quantum-Mechanically

(2012) Markus Sitzmann et al.   Journal of Chemical Information and Modeling

The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures

(2012) John Liebeschuetz et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structure-based design of nitrogen-linked macrocyclic kinase inhibitors leading to the clinical candidate SB1317/TG02, a potent inhibitor of cyclin dependant kinases (CDKs), Janus kinase 2 (JAK2), and Fms-like tyrosine kinase-3 (FLT3)

(2012) Anders Poulsen et al.   JOURNAL OF MOLECULAR MODELING

Biologically Active Macrocyclic Compounds - from Natural Products to Diversity-Oriented Synthesis

(2011) Charlotte M. Madsen et al.   EUROPEAN JOURNAL OF ORGANIC CHEMISTRY

Macrocycles Are Great Cycles: Applications, Opportunities, and Challenges of Synthetic Macrocycles in Drug Discovery

(2011) Eric Marsault et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

(2010) Paul Labute   Journal of Chemical Information and Modeling

Molecular Shape and Medicinal Chemistry: A Perspective

(2010) Anthony Nicholls et al.   JOURNAL OF MEDICINAL CHEMISTRY

Three-Dimensional Pharmacophore Methods in Drug Discovery

(2009) Andrew R. Leach et al.   JOURNAL OF MEDICINAL CHEMISTRY

Synthesis and Conformation−Activity Relationships of the Peptide Isosteres of FK228 and Largazole

(2009) Albert A. Bowers et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational study of ligand binding to protein receptors

(2008) Paul Wembridge et al.   BIOORGANIC CHEMISTRY

Conformational Sampling of Druglike Molecules with MOE and Catalyst: Implications for Pharmacophore Modeling and Virtual Screening

(2008) I-Jen Chen et al.   Journal of Chemical Information and Modeling

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

(2008) Edward M. Driggers et al.   NATURE REVIEWS DRUG DISCOVERY