相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand Binding Prediction in CSAR 2013 and 2014
Xiaolei Zhu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)
HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches
Sheng-You Huang et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)
Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise
Ashutosh Kumar et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)
Knowledge-Based Strategy to Improve Ligand Pose Prediction Accuracy for Lead Optimization
Cen Gao et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)
POSIT: Flexible Shape-Guided Docking For Pose Prediction
Brian P. Kelley et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)
PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity
Ambrish Roy et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)
Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock
Ann E. Cleves et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2015)
Improvements, trends, and new ideas in molecular docking: 2012-2013 in review
Elizabeth Yuriev et al.
JOURNAL OF MOLECULAR RECOGNITION (2015)
Hierarchical virtual screening approaches in small molecule drug discovery
Ashutosh Kumar et al.
METHODS (2015)
Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand
Samuel DeLuca et al.
PLOS ONE (2015)
Scaffold Hopping with Virtual Screening from IP3 to a Drug-Like Partial Agonist of the Inositol Trisphosphate Receptor
Sridhar R. Vasudevan et al.
CHEMBIOCHEM (2014)
PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions
Bingjie Hu et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2014)
The Application of Statistical Methods to Cognate Docking: A Path Forward?
Paul C. D. Hawkins et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)
Identification of 1,2,5-Oxadiazoles as a New Class of SENP2 Inhibitors Using Structure Based Virtual Screening
Ashutosh Kumar et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)
The SAMPL4 host-guest blind prediction challenge: an overview
Hari S. Muddana et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2014)
Molecular Similarity in Medicinal Chemistry
Gerald Maggiora et al.
JOURNAL OF MEDICINAL CHEMISTRY (2014)
PharmDock: a pharmacophore-based docking program
Bingjie Hu et al.
JOURNAL OF CHEMINFORMATICS (2014)
Computational Methods in Drug Discovery
Gregory Sliwoski et al.
PHARMACOLOGICAL REVIEWS (2014)
Virtual Screening Strategies in Drug Discovery: A Critical Review
A. Lavecchia et al.
CURRENT MEDICINAL CHEMISTRY (2013)
Scoring Functions for Prediction of Protein-Ligand Interactions
Jui-Chih Wang et al.
CURRENT PHARMACEUTICAL DESIGN (2013)
The holistic integration of virtual screening in drug discovery
Yusuf Tanrikulu et al.
DRUG DISCOVERY TODAY (2013)
CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series
Kelly L. Damm-Ganamet et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)
Exploring the Potential of Protein-Based Pharmacophore Models in Ligand Pose Prediction and Ranking
Bingjie Hu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)
Latest developments in molecular docking: 2010-2011 in review
Elizabeth Yuriev et al.
JOURNAL OF MOLECULAR RECOGNITION (2013)
Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures
Paul C. D. Hawkins et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)
FRED and HYBRID docking performance on standardized datasets
Mark McGann
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2012)
Discovery of a Novel and Potent Class of F. tularensis Enoyl-Reductase (FabI) Inhibitors by Molecular Shape and Electrostatic Matching
Kirk E. Hevener et al.
JOURNAL OF MEDICINAL CHEMISTRY (2012)
Integration of Ligand-Based Drug Screening with Structure-Based Drug Screening by Combining Maximum Volume Overlapping Score with Ligand Docking
Yoshifumi Fukunishi et al.
PHARMACEUTICALS (2012)
Overview of the CCP4 suite and current developments
Martyn D. Winn et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2011)
Current Trends in Virtual High Throughput Screening Using Ligand-Based and Structure-Based Methods
Nagamani Sukumar et al.
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING (2011)
State-of-the-art in ligand-based virtual screening
Peter Ripphausen et al.
DRUG DISCOVERY TODAY (2011)
SHAFTS: A Hybrid Approach for 3D Molecular Similarity Calculation. 1. Method and Assessment of Virtual Screening
Xiaofeng Liu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
Can We Trust Docking Results? Evaluation of Seven Commonly Used Programs on PDBbind Database
Dariusz Plewczynski et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
SHAFTS: A Hybrid Approach for 3D Molecular Similarity Calculation. 2. Prospective Case Study in the Discovery of Diverse p90 Ribosomal S6 Protein Kinase 2 Inhibitors To Suppress Cell Migration
Weiqiang Lu et al.
JOURNAL OF MEDICINAL CHEMISTRY (2011)
Challenges and advances in computational docking: 2009 in review
Elizabeth Yuriev et al.
JOURNAL OF MOLECULAR RECOGNITION (2011)
RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
Sarel J. Fleishman et al.
PLOS ONE (2011)
Pathway and mechanism of drug binding to G-protein-coupled receptors
Ron O. Dror et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
Ignasi Buch et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Computational Approaches for Fragment-Based and De Novo Design
Kathryn Loving et al.
CURRENT TOPICS IN MEDICINAL CHEMISTRY (2010)
De novo design: balancing novelty and confined chemical space
Peter S. Kutchukian et al.
EXPERT OPINION ON DRUG DISCOVERY (2010)
Protein Kinases: Docking and Homology Modeling Reliability
Tiziano Tuccinardi et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)
Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database
Paul C. D. Hawkins et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)
Extended-Connectivity Fingerprints
David Rogers et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)
Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions
Sheng-You Huang et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2010)
Structure-Based Drug Screening and Ligand-Based Drug Screening with Machine Learning
Yoshifumi Fukunishi
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING (2009)
APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening
Violeta I. Perez-Nueno et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)
ROSETTALIGAND Docking with Full Ligand and Receptor Flexibility
Ian W. Davis et al.
JOURNAL OF MOLECULAR BIOLOGY (2009)
Identification of a chemical probe for NAADP by virtual screening
Edmund Naylor et al.
NATURE CHEMICAL BIOLOGY (2009)
Blind docking of pharmaceutically relevant compounds using RosettaLigand
Ian W. Davis et al.
PROTEIN SCIENCE (2009)
How to do an evaluation: pitfalls and traps
Paul C. D. Hawkins et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2008)
Prediction of protein-ligand complex structure by docking software guided by other complex structures
Yoshifumi Fukunishi et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2008)
Synergies of virtual screening approaches
Ingo Muegge
MINI-REVIEWS IN MEDICINAL CHEMISTRY (2008)
Comparison of shape-matching and docking as virtual screening tools
Paul C. D. Hawkins et al.
JOURNAL OF MEDICINAL CHEMISTRY (2007)
Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
Gilles Marcou et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2007)
ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility
Jens Meiler et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
Richard A. Friesner et al.
JOURNAL OF MEDICINAL CHEMISTRY (2006)
A critical assessment of docking programs and scoring functions
Gregory L. Warren et al.
JOURNAL OF MEDICINAL CHEMISTRY (2006)
Knowledge-based interaction fingerprint scoring: A simple method for improving the effectiveness of fast scoring functions
CP Mpamhanga et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2006)
A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction
TS Rush et al.
JOURNAL OF MEDICINAL 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)
Structural interaction fingerprint (SIFt): A novel method for analyzing three-dimensional protein-ligand binding interactions
Z Deng et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
CORES: An automated method for generating three-dimensional models of protein/ligand complexes
BJ Hare et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): Evaluation of performance
A Bender et al.
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2004)
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
E Krissinel et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2004)
SDOCKER: A method utilizing existing X-ray structures to improve docking accuracy
GS Wu et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
Expanded interaction fingerprint method for analyzing ligand binding modes in docking and structure-based drug design
MD Kelly et al.
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2004)
Gaussian docking functions
MR McGann et al.
BIOPOLYMERS (2003)
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
A Jakalian et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
The Protein Data Bank
HM Berman et al.
NUCLEIC ACIDS RESEARCH (2000)
分享论文
