DOCK 6: Impact of new features and current docking performance

Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design

(2014) William J. Allen et al.   Journal of Chemical Information and Modeling

Pharmacophore-Based Similarity Scoring for DOCK

(2014) Lingling Jiang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

(2014) Marcus Fischer et al.   Nature Chemistry

Effect of Mutations at Position E138 in HIV-1 Reverse Transcriptase and Their Interactions with the M184I Mutation on Defining Patterns of Resistance to Nonnucleoside Reverse Transcriptase Inhibitors Rilpivirine and Etravirine

(2013) Hong-Tao Xu et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Improving the Scoring of Protein–Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization

(2013) Jinfeng Liu et al.   Journal of Chemical Information and Modeling

CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series

(2013) Kelly L. Damm-Ganamet et al.   Journal of Chemical Information and Modeling

CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys

(2013) James B. Dunbar et al.   Journal of Chemical Information and Modeling

Grid-based molecular footprint comparison method for docking andde novodesign: Application to HIVgp41

(2013) Trent E. Balius et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Discovery of Highly Potent Microsomal Prostaglandin E2 Synthase 1 Inhibitors Using the Active Conformation Structural Model and Virtual Screen

(2013) Shan He et al.   JOURNAL OF MEDICINAL CHEMISTRY

Latest developments in molecular docking: 2010-2011 in review

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

Ligand Pose and Orientational Sampling in Molecular Docking

(2013) Ryan G. Coleman et al.   PLoS One

Distinct resistance patterns to etravirine and rilpivirine in viruses containing nonnucleoside reverse transcriptase inhibitor mutations at baseline

(2012) Eugene L. Asahchop et al.   AIDS

A Water-Based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases

(2012) Yulin Huang et al.   BIOCHEMISTRY

Footprint-based identification of viral entry inhibitors targeting HIVgp41

(2012) Patrick M. Holden et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Identification of novel antimycobacterial chemical agents through the in silico multi-conformational structure-based drug screening of a large-scale chemical library

(2012) Yuji Koseki et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Genotypic resistance profiles associated with virological failure to darunavir-containing regimens: a cross-sectional analysis

(2012) G. Sterrantino et al.   INFECTION

Protein Flexibility in Virtual Screening: The BACE-1 Case Study

(2012) Sandro Cosconati et al.   Journal of Chemical Information and Modeling

ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader

(2012) Manuel Rueda et al.   Journal of Chemical Information and Modeling

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

(2012) Jin Yu Xiang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Evaluation of DOCK 6 as a pose generation and database enrichment tool

(2012) Scott R. Brozell et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Surflex-Dock: Docking benchmarks and real-world application

(2012) Russell Spitzer et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor

(2012) S Yoshikawa et al.   ONCOGENE

Targeting Fatty Acid Binding Protein (FABP) Anandamide Transporters – A Novel Strategy for Development of Anti-Inflammatory and Anti-Nociceptive Drugs

(2012) William T. Berger et al.   PLoS One

Small molecule inhibitors of SHP2 tyrosine phosphatase discovered by virtual screening

(2011) Zhi-Hong Yu et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

A Call to Arms: What You Can Do for Computational Drug Discovery

(2011) Heather A. Carlson et al.   Journal of Chemical Information and Modeling

Molecular Docking with Ligand Attached Water Molecules

(2011) Mette A. Lie et al.   Journal of Chemical Information and Modeling

FRED Pose Prediction and Virtual Screening Accuracy

(2011) Mark McGann   Journal of Chemical Information and Modeling

Implementation and evaluation of a docking-rescoring method using molecular footprint comparisons

(2011) Trent E. Balius et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking

(2011) Stefano Forli et al.   JOURNAL OF MEDICINAL CHEMISTRY

Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the “Hydrophobic Wall” of Carbonic Anhydrase

(2011) Jasmin Mecinović et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Identification of Inhibitors against Mycobacterium tuberculosis Thiamin Phosphate Synthase, an Important Target for the Development of Anti-TB Drugs

(2011) Garima Khare et al.   PLoS One

Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase

(2011) P. W. Snyder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic placement of structural water molecules for improved scoring of protein-ligand interactions

(2011) D. J. Huggins et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Lersivirine, a Nonnucleoside Reverse Transcriptase Inhibitor with Activity against Drug-Resistant Human Immunodeficiency Virus Type 1

(2010) R. Corbau et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

HIV-1 Protease Mutations and Protease Inhibitor Cross-Resistance

(2010) S.-Y. Rhee et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Origins of Resistance to the HIVgp41 Viral Entry Inhibitor T20

(2010) Brian E. McGillick et al.   BIOCHEMISTRY

Computer-aided drug-discovery techniques that account for receptor flexibility

(2010) Jacob D Durrant et al.   CURRENT OPINION IN PHARMACOLOGY

Differential impact of the HIV-1 non-nucleoside reverse transcriptase inhibitor mutations K103N and M230L on viral replication and enzyme function

(2010) H.-T. Xu et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Docking Validation Resources: Protein Family and Ligand Flexibility Experiments

(2010) Sudipto Mukherjee et al.   Journal of Chemical Information and Modeling

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

TMC278, a Next-Generation Nonnucleoside Reverse Transcriptase Inhibitor (NNRTI), Active against Wild-Type and NNRTI-Resistant HIV-1

(2009) H. Azijn et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Design and Biological Evaluation of Novel, Balanced Dual PPARα/γ Agonists

(2009) Uwe Grether et al.   ChemMedChem

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The Impact of Individual Human Immunodeficiency Virus Type 1 Protease Mutations on Drug Susceptibility Is Highly Influenced by Complex Interactions with the Background Protease Sequence

(2009) H. Van Marck et al.   JOURNAL OF VIROLOGY

Docking for fragment inhibitors of AmpC  -lactamase

(2009) D. G. Teotico et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DOCK 6: Combining techniques to model RNA-small molecule complexes

(2009) P. T. Lang et al.   RNA

Pattern and impact of emerging resistance mutations in treatment experienced patients failing darunavir-containing regimen

(2008) Constance Delaugerre et al.   AIDS

Discovery of novel 4-amino-6-arylaminopyrimidine-5-carbaldehyde oximes as dual inhibitors of EGFR and ErbB-2 protein tyrosine kinases

(2008) Guozhang Xu et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

4-Amino-6-arylamino-pyrimidine-5-carbaldehyde hydrazones as potent ErbB-2/EGFR dual kinase inhibitors

(2008) Guozhang Xu et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Flexible ligand docking to multiple receptor conformations: a practical alternative

(2008) Maxim Totrov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Exploiting Ordered Waters in Molecular Docking

(2008) Niu Huang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structural Basis for the Improved Drug Resistance Profile of New Generation Benzophenone Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors†

(2008) Jingshan Ren et al.   JOURNAL OF MEDICINAL CHEMISTRY

Thermodynamic and Structure Guided Design of Statin Based Inhibitors of 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase

(2008) Ronald W. Sarver et al.   JOURNAL OF MEDICINAL CHEMISTRY

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

(2008) Alan P. Graves et al.   JOURNAL OF MOLECULAR BIOLOGY

Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

(2008) Robert Abel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: Strategic flexibility explains potency against resistance mutations

(2008) K. Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA