Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction

Novel human mPGES-1 inhibitors identified through structure-based virtual screening

(2011) Adel Hamza et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Computational study of bindings of HL9, a nonapeptide fragment of human lysozyme, to HIV-1 fusion protein gp41

(2011) Yossa Dwi Hartono et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular modelling studies on Arylthioindoles as potent inhibitors of tubulin polymerization

(2011) Antonio Coluccia et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Solvent Interaction Energy Calculations on Molecular Dynamics Trajectories: Increasing the Efficiency Using Systematic Frame Selection

(2011) Markus A. Lill et al.   Journal of Chemical Information and Modeling

CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes

(2011) James B. Dunbar et al.   Journal of Chemical Information and Modeling

CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions

(2011) Richard D. Smith et al.   Journal of Chemical Information and Modeling

Solvated Interaction Energy (SIE) for Scoring Protein–Ligand Binding Affinities. 2. Benchmark in the CSAR-2010 Scoring Exercise

(2011) Traian Sulea et al.   Journal of Chemical Information and Modeling

Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain

(2011) Victor M. Anisimov et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Exploring the Size Limit of Templates for Inhibitors of the M2 Ion Channel of Influenza A Virus

(2011) María D. Duque et al.   JOURNAL OF MEDICINAL CHEMISTRY

New Ultrahigh Affinity Host−Guest Complexes of Cucurbit[7]uril with Bicyclo[2.2.2]octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations

(2011) Sarvin Moghaddam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Modeling aqueous solvation with semi-explicit assembly

(2011) C. J. Fennell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure–activity relationship of novel DAPK inhibitors identified by structure-based virtual screening

(2010) Masako Okamoto et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations

(2010) Navnit Kumar Mishra et al.   CARBOHYDRATE RESEARCH

Theoretical study on the HIV-1 integrase–5CITEP complex based on polarized force fields

(2010) Caiyi Wei et al.   CHEMICAL PHYSICS LETTERS

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model

(2010) Christopher R. Corbeil et al.   Journal of Chemical Theory and Computation

Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge

(2010) Enrico O. Purisima et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Acyclic Cucurbit[n]uril Congeners Are High Affinity Hosts

(2010) Da Ma et al.   JOURNAL OF ORGANIC CHEMISTRY

Computational Determination of Binding Structures and Free Energies of Phosphodiesterase-2 with Benzo[1,4]diazepin-2-one Derivatives

(2010) Bo Yang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Predictions of Binding for Dopamine D2 Receptor Antagonists by the SIE Method

(2009) Yeng-Tseng Wang et al.   Journal of Chemical Information and Modeling

Docking Ligands into Flexible and Solvated Macromolecules. 4. Are Popular Scoring Functions Accurate for this Class of Proteins?

(2009) Pablo Englebienne et al.   Journal of Chemical Information and Modeling

Large-Scale Application of High-Throughput Molecular Mechanics with Poisson−Boltzmann Surface Area for Routine Physics-Based Scoring of Protein−Ligand Complexes

(2009) Scott P. Brown et al.   JOURNAL OF MEDICINAL CHEMISTRY

Importance of oligomerisation on Pseudomonas aeruginosaLectin-II binding affinity. In silico and in vitro mutagenesis

(2009) Michaela Wimmerová et al.   JOURNAL OF MOLECULAR MODELING

Restoring Charge Asymmetry in Continuum Electrostatics Calculations of Hydration Free Energies

(2009) Enrico O. Purisima et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Host−Guest Complexes with Protein−Ligand-like Affinities: Computational Analysis and Design

(2009) Sarvin Moghaddam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Oil/Water Transfer Is Partly Driven by Molecular Shape, Not Just Size

(2009) Christopher J. Fennell et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Stability and ATP Binding of the Nucleotide-binding Domain of the Wilson Disease Protein: Effect of the Common H1069Q Mutation

(2008) Agustina Rodriguez-Granillo et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Dynamics—Solvated Interaction Energy Studies of Protein–Protein Interactions: The MP1–p14 Scaffolding Complex

(2008) Qizhi Cui et al.   JOURNAL OF MOLECULAR BIOLOGY

Charge Asymmetries in Hydration of Polar Solutes

(2008) David L. Mobley et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go

(2007) N Moitessier et al.   BRITISH JOURNAL OF PHARMACOLOGY