High-throughput quantum-mechanics/molecular-mechanics (ONIOM) macromolecular crystallographic refinement with PHENIX/DivCon: the impact of mixed Hamiltonian methods on ligand and protein structure

Validation of ligands in macromolecular structures determined by X-ray crystallography

(2018) Oliver S. Smart et al.   Acta Crystallographica Section D-Structural Biology

On the Difference Between Additive and Subtractive QM/MM Calculations

(2018) Lili Cao et al.   Frontiers in Chemistry

Keep it together: restraints in crystallographic refinement of macromolecule–ligand complexes

(2017) Roberto A. Steiner et al.   Acta Crystallographica Section D-Structural Biology

Ligand complex structures in protein crystallography

(2017) Judit É. Debreczeni et al.   Acta Crystallographica Section D-Structural Biology

Ligand fitting with CCP4

(2017) Robert A. Nicholls   Acta Crystallographica Section D-Structural Biology

AceDRG: a stereochemical description generator for ligands

(2017) Fei Long et al.   Acta Crystallographica Section D-Structural Biology

Protein crystallography and drug discovery: recollections of knowledge exchange between academia and industry

(2017) Tom L. Blundell   IUCrJ

Molprobity's ultimate rotamer-library distributions for model validation

(2016) Bradley J. Hintze et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

(2016) Sérgio Filipe Sousa et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

The Cambridge Structural Database

(2016) Colin R. Groom et al.   Acta Crystallographica Section B-Structural Science Crystal Engineering and Materials

Improved ligand geometries in crystallographic refinement usingAFITTinPHENIX

(2016) Pawel A. Janowski et al.   Acta Crystallographica Section D-Structural Biology

XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement

(2016) Oleg Borbulevych et al.   Acta Crystallographica Section D-Structural Biology

The ONIOM Method and Its Applications

(2015) Lung Wa Chung et al.   CHEMICAL REVIEWS

Validation of small- and macromolecular X-ray structures: PDB and CCDC collaborations

(2015) S. Gore et al.   ACTA CRYSTALLOGRAPHICA SECTION A

Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

(2014) Nigel W. Moriarty et al.   FEBS Journal

QM/MM through the 1990s: The First Twenty Years of Method Development and Applications

(2014) Meiyi Liu et al.   ISRAEL JOURNAL OF CHEMISTRY

Protein–Ligand Cocrystal Structures: We Can Do Better

(2014) Charles H. Reynolds   ACS Medicinal Chemistry Letters

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics programDivConinto thePHENIXrefinement package

(2014) Oleg Y. Borbulevych et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures

(2013) Edwin Pozharski et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions

(2013) Jiří Hostaš et al.   CHEMICAL PHYSICS LETTERS

Latest developments in molecular docking: 2010-2011 in review

(2013) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

Statistical quality indicators for electron-density maps

(2012) Ian J. Tickle   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Towards automated crystallographic structure refinement withphenix.refine

(2012) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters

(2012) James J. P. Stewart   JOURNAL OF MOLECULAR MODELING

X-ray crystallography: assessment and validation of protein–small molecule complexes for drug discovery

(2011) David R Cooper et al.   Expert Opinion on Drug Discovery

On the Convergence of QM/MM Energies

(2011) LiHong Hu et al.   Journal of Chemical Theory and Computation

Accurate assessment of the strain energy in a protein-bound drug using QM/MM X-ray refinement and converged quantum chemistry

(2011) Zheng Fu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks

(2011) Nikolay V. Plotnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A New Generation of Crystallographic Validation Tools for the Protein Data Bank

(2011) Randy J. Read et al.   STRUCTURE

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Quantum Mechanical Pairwise Decomposition Analysis of Protein Kinase B Inhibitors: Validating a New Tool for Guiding Drug Design

(2010) Xiaohua Zhang et al.   Journal of Chemical Information and Modeling

Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes

(2010) Alpeshkumar K. Malde et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

QM/MM X-ray refinement of zinc metalloenzymes

(2010) Xue Li et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

Computational alanine scanning with linear scaling semiempirical quantum mechanical methods

(2010) David J. Diller et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Automated minimization of steric clashes in protein structures

(2010) Srinivas Ramachandran et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

electronic Ligand Builder and Optimization Workbench(eLBOW): a tool for ligand coordinate and restraint generation

(2009) Nigel W. Moriarty et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes

(2009) Jan Řezáč et al.   Journal of Chemical Theory and Computation

AM1 Parameters for the Prediction of1H and13C NMR Chemical Shifts in Proteins†

(2009) Duane E. Williams et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Assessment of the protein-structure refinement category in CASP8

(2009) Justin L. MacCallum et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

Application of the PM6 method to modeling proteins

(2008) James J. P. Stewart   JOURNAL OF MOLECULAR MODELING

Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures

(2008) Paul Labute   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS