Automated docking for novel drug discovery

Structure and dynamics of β-lactoglobulin in complex with dodecyl sulfate and laurate: A molecular dynamics study

(2012) Martiniano Bello et al.   BIOPHYSICAL CHEMISTRY

Ligand Based Pharmacophore Identification and Molecular Docking Studies for Grb2 Inhibitors

(2012) Venkatesh Arulalapperumal et al.   BULLETIN OF THE KOREAN CHEMICAL SOCIETY

Modeling loop backbone flexibility in receptor-ligand docking simulations

(2012) Johannes Flick et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors

(2012) Ori Kalid et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Docking and DFT Studies to explore the Topoisomerase II ATP Pocket employing 3-Substituted 2,6-Piperazindiones for drug design

(2012) J. Correa-Basurto et al.   MOLECULAR SIMULATION

Molecular Dynamics of a Thermostable Multicopper Oxidase from Thermus thermophilus HB27: Structural Differences between the Apo and Holo Forms

(2012) Martiniano Bello et al.   PLoS One

ReFlexIn: A Flexible Receptor Protein-Ligand Docking Scheme Evaluated on HIV-1 Protease

(2012) Simon Leis et al.   PLoS One

Effect of the explicit flexibility of the InhA enzyme from Mycobacterium tuberculosis in molecular docking simulations

(2011) Elisangela ML Cohen et al.   BMC GENOMICS

Disparate Degrees of Hypervariable Loop Flexibility Control T-Cell Receptor Cross-Reactivity, Specificity, and Binding Mechanism

(2011) Daniel R. Scott et al.   JOURNAL OF MOLECULAR BIOLOGY

Enrichment of virtual hits by progressive shape-matching and docking

(2011) Jiwon Choi et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Multilevel Parallelization of AutoDock 4.2

(2011) Andrew P Norgan et al.   Journal of Cheminformatics

Homology modeling and molecular dynamics of CYP1A1 and CYP2B1 to explore the metabolism of aryl derivatives by docking and experimental assays

(2010) Martha C. Rosales-Hernández et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Virtual screening with AutoDock: theory and practice

(2010) Sandro Cosconati et al.   Expert Opinion on Drug Discovery

Advances and Challenges in Protein-Ligand Docking

(2010) Sheng-You Huang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes

(2010) Xun Li et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular docking and molecular dynamics simulation studies of GPR40 receptor–agonist interactions

(2010) Shao-Yong Lu et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions

(2010) Sheng-You Huang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina

(2010) Max W. Chang et al.   PLoS One

Flexible ligand docking using conformational ensembles

(2010) David M. Lorber et al.   PROTEIN SCIENCE

MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening

(2009) Nicolas Sauton et al.   BMC BIOINFORMATICS

Natural products and drug discovery. Can thousands of years of ancient medical knowledge lead us to new and powerful drug combinations in the fight against cancer and dementia?

(2009) Hong-Fang Ji et al.   EMBO REPORTS

Rational drug design

(2009) Soma Mandal et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Blind docking of 260 protein-ligand complexes with EADock 2.0

(2009) Aurélien Grosdidier et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

(2009) Noriaki Okimoto et al.   PLoS Computational Biology

Structural studies of human purine nucleoside phosphorylase: Towards a new specific empirical scoring function

(2008) Luis Fernando Saraiva Macedo Timmers et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Accommodation of GDP-Linked Sugars in the Active Site of GDP-Perosamine Synthase†,‡

(2008) Paul D. Cook et al.   BIOCHEMISTRY

Molecular Docking Algorithms

(2008) Raquel Dias et al.   CURRENT DRUG TARGETS

Overcoming the challenges of membrane protein crystallography

(2008) Elisabeth P Carpenter et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Lead Finder: An Approach To Improve Accuracy of Protein−Ligand Docking, Binding Energy Estimation, and Virtual Screening

(2008) Oleg V. Stroganov et al.   Journal of Chemical Information and Modeling

Fully Automated Molecular Mechanics Based Induced Fit Protein−Ligand Docking Method

(2008) Jürgen Koska et al.   Journal of Chemical Information and Modeling

MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening

(2008) Shuangye Yin et al.   Journal of Chemical Information and Modeling

Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints

(2008) Michal Brylinski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Agonist-Induced Conformational Changes in Bovine Rhodopsin: Insight into Activation of G-Protein-Coupled Receptors

(2008) Supriyo Bhattacharya et al.   JOURNAL OF MOLECULAR BIOLOGY