Improving the accuracy of the FMO binding affinity prediction of ligand-receptor complexes containing metals

SophosQM: Accurate Binding Affinity Prediction in Compound Optimization

(2023) Riccardo Guareschi et al.   ACS Omega

IRMPD spectroscopy and quantum-chemical simulations of the reaction products of cisplatin with the dipeptide CysGly

(2023) Davide Corinti et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

Homodimeric complexes of the 90–231 human prion: a multilayered computational study based on FMO/GRID-DRY approach

(2022) Roberto Paciotti et al.   JOURNAL OF MOLECULAR MODELING

The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study

(2022) Roberto Paciotti et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Development of the FMO/RI-MP2 Fully Analytic Gradient Using a Hybrid-Distributed/Shared Memory Programming Model

(2020) Buu Q. Pham et al.   Journal of Chemical Theory and Computation

Recent developments in the general atomic and molecular electronic structure system

(2020) Giuseppe M. J. Barca et al.   JOURNAL OF CHEMICAL PHYSICS

Characterization of PD-L1 binding sites by a combined FMO/GRID-DRY approach

(2020) Roberto Paciotti et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Three-Body Energy Decomposition Analysis Based on the Fragment Molecular Orbital Method

(2020) Dmitri G. Fedorov   JOURNAL OF PHYSICAL CHEMISTRY A

The MDM2 inducible promoter folds into four-tetrad antiparallel G-quadruplexes targetable to fight malignant liposarcoma

(2020) Sara Lago et al.   NUCLEIC ACIDS RESEARCH

GFN2-xTB—An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions

(2019) Christoph Bannwarth et al.   Journal of Chemical Theory and Computation

Structure Optimisation of large Transition Metal Complexes with extended Tight-Binding Methods

(2019) Markus Bursch et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Solvent Screening in Zwitterions Analyzed with the Fragment Molecular Orbital Method

(2019) Dmitri G. Fedorov   Journal of Chemical Theory and Computation

Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study

(2018) Yoshio Okiyama et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Down-Regulation of the Androgen Receptor by G-Quadruplex Ligands Sensitizes Castration-Resistant Prostate Cancer Cells to Enzalutamide

(2018) Martina Tassinari et al.   JOURNAL OF MEDICINAL CHEMISTRY

An insight of early PrP-E200K aggregation by combined molecular dynamics/fragment molecular orbital approaches

(2018) Roberto Paciotti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Robust and Accurate Tight-Binding Quantum Chemical Method for Structures, Vibrational Frequencies, and Noncovalent Interactions of Large Molecular Systems Parametrized for All spd-Block Elements (Z = 1–86)

(2017) Stefan Grimme et al.   Journal of Chemical Theory and Computation

Quadruplex nucleic acids as targets for anticancer therapeutics

(2017) Stephen Neidle   Nature Reviews Chemistry

Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein–Ligand Binding in Solution

(2016) Dmitri G. Fedorov et al.   JOURNAL OF PHYSICAL CHEMISTRY A

The role of alkali metal cations in the stabilization of guanine quadruplexes: why K+ is the best

(2016) F. Zaccaria et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Investigation of the molecular similarity in closely related protein systems: The PrP case study

(2015) Loriano Storchi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Use of Many-Body Expansions and Geometry Optimizations in Fragment-Based Methods

(2014) Dmitri G. Fedorov et al.   ACCOUNTS OF CHEMICAL RESEARCH

Use of an auxiliary basis set to describe the polarization in the fragment molecular orbital method

(2014) Dmitri G. Fedorov et al.   CHEMICAL PHYSICS LETTERS

Caffeine-Based Gold(I) N-Heterocyclic Carbenes as Possible Anticancer Agents: Synthesis and Biological Properties

(2014) Benoît Bertrand et al.   INORGANIC CHEMISTRY

Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition

(2014) T. Hayashi et al.   NUCLEIC ACIDS RESEARCH

Selective G-quadruplex stabilizers: Schiff-base metal complexes with anticancer activity

(2014) Alessio Terenzi et al.   RSC Advances

GAMESS As a Free Quantum-Mechanical Platform for Drug Research

(2013) Yuri Alexeev et al.   CURRENT TOPICS IN 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

Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: a comprehensive quantum chemical approach

(2013) Yevgen P. Yurenko et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Salphen metal complexes as tunable G-quadruplex binders and optical probes

(2013) Nurul H. Abd Karim et al.   RSC Advances

Assessing the Differential Affinity of Small Molecules for Noncanonical DNA Structures

(2012) Loic Stefan et al.   CHEMBIOCHEM

RI-MP2 Gradient Calculation of Large Molecules Using the Fragment Molecular Orbital Method

(2012) Takeshi Ishikawa et al.   Journal of Physical Chemistry Letters

Energy Decomposition Analysis in Solution Based on the Fragment Molecular Orbital Method

(2011) Dmitri G. Fedorov et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Making sense of G-quadruplex and i-motif functions in oncogene promoters

(2010) Tracy A. Brooks et al.   FEBS Journal

Molecular tailoring approach in conjunction with MP2 and Ri-MP2 codes: A comparison with fragment molecular orbital method

(2010) Anuja P. Rahalkar et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods†

(2010) Casper Steinmann et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Systematic Study of the Embedding Potential Description in the Fragment Molecular Orbital Method†

(2010) Dmitri G. Fedorov et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Revised model core potentials for third-row transition–metal atoms from Lu to Hg

(2009) Hirotoshi Mori et al.   CHEMICAL PHYSICS LETTERS

Fragment molecular orbital calculation using the RI-MP2 method

(2009) Takeshi Ishikawa et al.   CHEMICAL PHYSICS LETTERS

Derivatives of the approximated electrostatic potentials in the fragment molecular orbital method

(2009) Takeshi Nagata et al.   CHEMICAL PHYSICS LETTERS

Heterogeneous conductorlike solvation model

(2009) Dejun Si et al.   JOURNAL OF CHEMICAL PHYSICS