Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls

Computational thermodynamics, computational kinetics, and materials design

(2014) Xiao-Gang Lu et al.   CHINESE SCIENCE BULLETIN

Recent Advances in Computer-Aided Drug Design as Applied to Anti-Influenza Drug Discovery

(2014) Prema Mallipeddi et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Structure-Based Virtual Screening Approach for Discovery of Covalently Bound Ligands

(2014) Dora Toledo Warshaviak et al.   Journal of Chemical Information and Modeling

Prediction of Substrates for Glutathione Transferases by Covalent Docking

(2014) Guang Qiang Dong et al.   Journal of Chemical Information and Modeling

Docking Covalent Inhibitors: A Parameter Free Approach To Pose Prediction and Scoring

(2014) Kai Zhu et al.   Journal of Chemical Information and Modeling

Intelligent Computational Nanotechnology: The Role of Computational Intelligence in the Development of Nanoscience and Nanotechnology

(2014) Omar Paranaiba Vilela Neto   Journal of Computational and Theoretical Nanoscience

An introduction to biomolecular simulations and docking

(2014) Cameron Mura et al.   MOLECULAR SIMULATION

Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction

(2014) Kai Zhu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Benchmarking in Vitro Covalent Binding Burden As a Tool To Assess Potential Toxicity Caused by Nonspecific Covalent Binding of Covalent Drugs

(2013) Upendra P. Dahal et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity

(2013) Bahareh Honarparvar et al.   CHEMICAL REVIEWS

Docking-Based Virtual Screening of Covalently Binding Ligands: An Orthogonal Lead Discovery Approach

(2013) Jörg Schröder et al.   JOURNAL OF MEDICINAL CHEMISTRY

Latest developments in molecular docking: 2010-2011 in review

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

Identification of irreversible protein splicing inhibitors as potential anti-TB drugs: insight from hybrid non-covalent/covalent docking virtual screening and molecular dynamics simulations

(2013) Lauren Blake et al.   MEDICINAL CHEMISTRY RESEARCH

A conceptual framework for computational models of Achilles tendon homeostasis

(2013) David W. Smith et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Drugging Topoisomerases: Lessons and Challenges

(2012) Yves Pommier   ACS Chemical Biology

Nanoparticle mediated non-covalent drug delivery

(2012) Tennyson Doane et al.   ADVANCED DRUG DELIVERY REVIEWS

Lead optimization studies towards the discovery of novel carbamates as potent AChE inhibitors for the potential treatment of Alzheimer’s disease

(2012) Kuldeep K. Roy et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Drug discovery for a new generation of covalent drugs

(2012) Amit S Kalgutkar et al.   Expert Opinion on Drug Discovery

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

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

CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints

(2012) Xuchang Ouyang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Accessible High-Throughput Virtual Screening Molecular Docking Software for Students and Educators

(2012) Reed B. Jacob et al.   PLoS Computational Biology

Novel inhibitors of glyceraldehyde-3-phosphate dehydrogenase: Covalent modification of NAD-binding site by aromatic thiols

(2011) K. A. Chernorizov et al.   BIOCHEMISTRY-MOSCOW

Fragment-Based Drug Design: Computational and Experimental State of the Art

(2011) Laurent Hoffer et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Synthesis and SAR Study of Novel Peptide Aldehydes as Inhibitors of 20S Proteasome

(2011) Yuheng Ma et al.   MOLECULES

The resurgence of covalent drugs

(2011) Juswinder Singh et al.   NATURE REVIEWS DRUG DISCOVERY

Virtual screening with AutoDock: theory and practice

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

In silico fragment-based drug design

(2010) Zenon D Konteatis   Expert Opinion on Drug Discovery

Structural ensemble in computational drug screening

(2010) Yoshifumi Fukunishi   Expert Opinion on Drug Metabolism & Toxicology

Synthesis, in Vitro and in Vivo Biological Evaluation, Docking Studies, and Structure−Activity Relationship (SAR) Discussion of Dipeptidyl Boronic Acid Proteasome Inhibitors Composed of β-Amino Acids

(2010) Yongqiang Zhu et al.   JOURNAL OF MEDICINAL CHEMISTRY

Challenges and advances in computational docking: 2009 in review

(2010) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

Second-Generation Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors in Non-small Cell Lung Cancer

(2010) Gregory J. Riely   Journal of Thoracic Oncology

Docking, virtual high throughput screening and in silico fragment-based drug design

(2009) Vincent Zoete et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Docking and 3D-QSAR Studies on Isatin Sulfonamide Analogues as Caspase-3 Inhibitors

(2009) Qi Wang et al.   Journal of Chemical Information and Modeling

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Automated Docking Screens: A Feasibility Study

(2009) John J. Irwin et al.   JOURNAL OF MEDICINAL CHEMISTRY

Constrained Peptidomimetics Reveal Detailed Geometric Requirements of Covalent Prolyl Oligopeptidase Inhibitors

(2009) Janice Lawandi et al.   JOURNAL OF MEDICINAL CHEMISTRY

Covalent Modifiers: An Orthogonal Approach to Drug Design

(2009) Michele H. Potashman et al.   JOURNAL OF MEDICINAL CHEMISTRY

Covalent complexes of proteasome model with peptide aldehyde inhibitors MG132 and MG101: docking and molecular dynamics study

(2009) Siwei Zhang et al.   JOURNAL OF MOLECULAR MODELING

Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking

(2009) P Benjamin Juhl et al.   BMC STRUCTURAL BIOLOGY

Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock

(2009) Zsolt Bikadi et al.   Journal of Cheminformatics

The Development of HKI‐272 and Related Compounds for the Treatment of Cancer

(2008) Allan Wissner et al.   ARCHIV DER PHARMAZIE

Docking and Biomolecular Simulations on Computer Grids: Status and Trends

(2008) Alexandru-Adrian Tantar et al.   Current Computer-Aided Drug Design

Application of dendrimer–drug complexation in the enhancement of drug solubility and bioavailability

(2008) Narendra K Jain et al.   Expert Opinion on Drug Metabolism & Toxicology

Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking

(2008) Giovanni Bottegoni et al.   JOURNAL OF MEDICINAL CHEMISTRY

Beyond Picomolar Affinities: Quantitative Aspects of Noncovalent and Covalent Binding of Drugs to Proteins

(2008) Adam J. T. Smith et al.   JOURNAL OF MEDICINAL CHEMISTRY

The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP

(2008) C.-H. Yun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA