Related references
Note: Only part of the references are listed.Surflex-Dock: Docking benchmarks and real-world application
Russell Spitzer et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2012)
Beta-secretase as a target for Alzheimer's disease drug discovery: an overview of in vitro methods for characterization of inhibitors
Francesca Mancini et al.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2011)
Combined SVM-based and docking-based virtual screening for retrieving novel inhibitors of c-Met
Qing-Qing Xie et al.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY (2011)
Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein-Ligand Binding Geometry and Free Energy
Obaidur Rahaman et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations
Tingjun Hou et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
Docking-based virtual screening for ligands of G protein-coupled receptors: Not only crystal structures but also in silico models
Santiago Vilar et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2011)
Insights on the Role of (Dis)order from Protein-Protein Interaction Linear Free-Energy Relationships
Meher K. Prakash
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)
The beta-secretase enzyme BACE1 as a therapeutic target for Alzheimer's disease
Robert Vassar et al.
ALZHEIMERS RESEARCH & THERAPY (2011)
Niemann-Pick type C cells show cholesterol dependent decrease of APP expression at the cell surface and its increased processing through the β-secretase pathway
Martina Malnar et al.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2010)
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
Pedro J. Ballester et al.
BIOINFORMATICS (2010)
Protein Thermostability Calculations Using Alchemical Free Energy Simulations
Daniel Seeliger et al.
BIOPHYSICAL JOURNAL (2010)
The Transcriptionally Active Amyloid Precursor Protein (APP) Intracellular Domain Is Preferentially Produced from the 695 Isoform of APP in a β-Secretase-dependent Pathway
Nikolai D. Belyaev et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2010)
Application of Fragment-Based NMR Screening, X-ray Crystallography, Structure-Based Design, and Focused Chemical Library Design to Identify Novel μM Leads for the Development of nM BACE-1 (β-Site APP Cleaving Enzyme 1) Inhibitors
Yu-Sen Wang et al.
JOURNAL OF MEDICINAL CHEMISTRY (2010)
Docking-Based Virtual Screening: Recent Developments
Tiziano Tuccinardi
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING (2009)
Comparative Assessment of Scoring Functions on a Diverse Test Set
Tiejun Cheng et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)
AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility
Garrett M. Morris et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
Homophilic interactions of the amyloid precursor protein (APP) ectodomain are regulated by the loop region and affect β-secretase cleavage of APP
Daniela Kaden et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2008)
β-secretase as a therapeutic target for Alzheimer's disease
Arun K. Ghosh et al.
NEUROTHERAPEUTICS (2008)
Impact of ligand protonation on virtual screening against ß-secretase (BACEI)
Timea Polgar et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2007)
2-amino-3,4-dihydroquinazolines as inhibitors of BACE-1 (β-site APP cleaving enzyme):: Use of structure based design to convert a micromolar hit into a nanomolar lead
Ellen W. Baxter et al.
JOURNAL OF MEDICINAL CHEMISTRY (2007)
Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
Ajay N. Jain
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2007)
Application of fragment screening by X-ray crystallography to β-secretase
Christopher W. Murray et al.
JOURNAL OF MEDICINAL CHEMISTRY (2007)
In silico binding free energy predictability by using the linear interaction energy (LIE) method: Bromobenzimidazole CK2 inhibitors as a case study
A. Bortolato et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2007)
Scoring functions and enrichment: a case study on Hsp90
Chrysi Konstantinou-Kirtay et al.
BMC BIOINFORMATICS (2007)
Discovering severe acute respiratory syndrome coronavirus 3CL protease inhibitors: Virtual screening, surface plasmon resonance, and fluorescence resonance energy transfer assays
Lili Chen et al.
JOURNAL OF BIOMOLECULAR SCREENING (2006)
Ensemble docking into flexible active sites.: Critical evaluation of FlexE against JNK-3 and β-secretase
Timea Polgar et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2006)
In silico discovery of β-secretase inhibitors
DZ Huang et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Chelate effect in cyclodextrin dimers:: A computational (MD, MM/PBSA, and MM/GBSA) study
I Beà et al.
JOURNAL OF ORGANIC CHEMISTRY (2006)
Virtual screening using binary kernel discrimination: Analysis of pesticide data
DJ Wilton et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2006)
Evaluation of binary QSAR models derived from LUDI and MOE scoring functions for structure based virtual screening
P Prathipati et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2006)
General and targeted statistical potentials for protein-ligand interactions
WTM Mooij et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
Virtual screening for β-secretase (BACE1) inhibitors reveals the importance of protonation states at Asp32 and Asp228
T Polgár et al.
JOURNAL OF MEDICINAL CHEMISTRY (2005)
LigScore:: a novel scoring function for predicting binding affinities
A Krammer et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2005)
Principal component analysis of trace elements in Serbian wheat
B Skrbic et al.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY (2005)
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
RA Friesner et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
TA Halgren et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
Identification of a small molecule nonpeptide active site β-secretase inhibitor that displays a nontraditional binding mode for aspartyl proteases
CA Coburn et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
A docking score function for estimating ligand-protein interactions: Application to acetylcholinesterase inhibition
JX Guo et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
Apo and inhibitor complex structures of BACE (β-secretase)
S Patel et al.
JOURNAL OF MOLECULAR BIOLOGY (2004)
Evaluation and application of multiple scoring functions for a virtual screening experiment
L Xing et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2004)
Virtual screening using protein-ligand docking: Avoiding artificial enrichment
ML Verdonk et al.
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2004)
Principal component and linear discriminant analyses of free amino acids and biogenic amines in Hungarian wines
K Héberger et al.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY (2003)
Improving structure-based virtual screening by multivariate analysis of scoring data
M Jacobsson et al.
JOURNAL OF MEDICINAL CHEMISTRY (2003)
A specific mechanism of nonspecific inhibition
SL McGovern et al.
JOURNAL OF MEDICINAL CHEMISTRY (2003)
Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling
RJ Rosenfeld et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2003)
Effect of detergent on promiscuous inhibitors
AJ Ryan et al.
JOURNAL OF MEDICINAL CHEMISTRY (2003)
Comparative evaluation of 11 scoring functions for molecular docking
RX Wang et al.
JOURNAL OF MEDICINAL CHEMISTRY (2003)
Comparison of ranking methods for virtual screening in lead-discovery programs
D Wilton et al.
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2003)
Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine
AN Jain
JOURNAL OF MEDICINAL CHEMISTRY (2003)
Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets?
C Bissantz et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)
Structure-based virtual screening: an overview
PD Lyne
DRUG DISCOVERY TODAY (2002)
Principles of docking: An overview of search algorithms and a guide to scoring functions
I Halperin et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2002)
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
RX Wang et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2002)
Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds
CS Ewig et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2001)
How does consensus scoring work for virtual library screening? An idealized computer experiment
RX Wang et al.
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2001)
A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities
GE Terp et al.
JOURNAL OF MEDICINAL CHEMISTRY (2001)
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
TJA Ewing et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2001)
Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations
C Bissantz et al.
JOURNAL OF MEDICINAL CHEMISTRY (2000)