4.4 Article

Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets

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。
Article Chemistry, Medicinal

Does a More Precise Chemical Description of Protein-Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?

Pedro J. Ballester et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)

Article Multidisciplinary Sciences

istar: A Web Platform for Large-Scale Protein-Ligand Docking

Hongjian Li et al.

PLOS ONE (2014)

Article Biochemical Research Methods

aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction

Douglas E. V. Pires et al.

BIOINFORMATICS (2013)

Review Chemistry, Multidisciplinary

Drug repositioning by structure-based virtual screening

Dik-Lung Ma et al.

CHEMICAL SOCIETY REVIEWS (2013)

Article Pharmacology & Pharmacy

Scoring Functions for Prediction of Protein-Ligand Interactions

Jui-Chih Wang et al.

CURRENT PHARMACEUTICAL DESIGN (2013)

Review Pharmacology & Pharmacy

The holistic integration of virtual screening in drug discovery

Yusuf Tanrikulu et al.

DRUG DISCOVERY TODAY (2013)

Article Chemistry, Medicinal

Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening

Jacob D. Durrant et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)

Article Chemistry, Medicinal

HotLig: A Molecular Surface-Directed Approach to Scoring Protein-Ligand Interactions

Sheng-Hung Wang et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)

Article Chemistry, Medicinal

ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein-Ligand Interactions

Guo-Bo Li et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)

Article Chemistry, Medicinal

Characterization of Small Molecule Binding. I. Accurate Identification of Strong Inhibitors in Virtual Screening

Bo Ding et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)

Article Biochemistry & Molecular Biology

A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function

Nadine Schneider et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2013)

Review Biochemistry & Molecular Biology

Latest developments in molecular docking: 2010-2011 in review

Elizabeth Yuriev et al.

JOURNAL OF MOLECULAR RECOGNITION (2013)

Review Pharmacology & Pharmacy

Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review

Tiejun Cheng et al.

AAPS JOURNAL (2012)

Review Pharmacology & Pharmacy

Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs

Lei Xie et al.

ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY, VOL 52 (2012)

Article Biochemical Research Methods

DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment

Andrea Volkamer et al.

BIOINFORMATICS (2012)

Review Multidisciplinary Sciences

Bioinformatics and variability in drug response: a protein structural perspective

Jennifer L. Lahti et al.

JOURNAL OF THE ROYAL SOCIETY INTERFACE (2012)

Article Multidisciplinary Sciences

Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification

Pedro J. Ballester et al.

JOURNAL OF THE ROYAL SOCIETY INTERFACE (2012)

Article Chemistry, Medicinal

CSAR Scoring Challenge Reveals the Need for New Concepts in Estimating Protein-Ligand Binding Affinity

Fedor N. Novikov et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Chemistry, Medicinal

Support Vector Regression Scoring of Receptor-Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries

Liwei Li et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Chemistry, Medicinal

Robust Scoring Functions for Protein-Ligand Interactions with Quantum Chemical Charge Models

Jui-Chih Wang et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Chemistry, Medicinal

A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing

Sarah L. Kinnings et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Chemistry, Medicinal

NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function

Jacob D. Durrant et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Chemistry, Medicinal

DSX: A Knowledge-Based Scoring Function for the Assessment of Protein-Ligand Complexes

Gerd Neudert et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Chemistry, Medicinal

Statistical Potential for Modeling and Ranking of Protein-Ligand Interactions

Hao Fan et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Chemistry, Medicinal

PHOENIX: A Scoring Function for Affinity Prediction Derived Using High-Resolution Crystal Structures and Calorimetry Measurements

Yat T. Tang et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Review Chemistry, Multidisciplinary

Can We Trust Docking Results? Evaluation of Seven Commonly Used Programs on PDBbind Database

Dariusz Plewczynski et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Article Biochemical Research Methods

BINANA: A novel algorithm for ligand-binding characterization

Jacob D. Durrant et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2011)

Review Pharmacology & Pharmacy

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

Stephanie Perot et al.

DRUG DISCOVERY TODAY (2010)

Article Chemistry, Medicinal

Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures

Sourav Das et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)

Article Chemistry, Medicinal

NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes

Jacob D. Durrant et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)

Article Chemistry, Medicinal

Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets

Christian Kramer et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)

Article Biochemistry & Molecular Biology

Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

Julien Michel et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2010)

Review Chemistry, Medicinal

Structure-Based Approaches to Target Fishing and Ligand Profiling

Didier Rognan

MOLECULAR INFORMATICS (2010)

Article Biotechnology & Applied Microbiology

Virtual screening: an endless staircase?

Gisbert Schneider

NATURE REVIEWS DRUG DISCOVERY (2010)

Article Chemistry, Physical

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)

Review Chemistry, Multidisciplinary

Efficient Drug Lead Discovery and Optimization

William L. Jorgensen

ACCOUNTS OF CHEMICAL RESEARCH (2009)

Article Chemistry, Medicinal

Comparative Assessment of Scoring Functions on a Diverse Test Set

Tiejun Cheng et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)

Article Chemistry, Multidisciplinary

AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility

Garrett M. Morris et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Multidisciplinary Sciences

Structure-based activity prediction for an enzyme of unknown function

Johannes C. Hermann et al.

NATURE (2007)

Article Chemistry, Medicinal

Comparison of topological, shape, and docking methods in virtual screening

Georgia B. McGaughey et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2007)

Article Chemistry, Medicinal

Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps

Andrew R. Leach et al.

JOURNAL OF MEDICINAL CHEMISTRY (2006)

Article Chemistry, Physical

Molecular mechanics methods for predicting protein-ligand binding

Niu Huang et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2006)

Article Chemistry, Medicinal

Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes

A Oda et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2006)

Article Chemistry, Medicinal

PostDOCK: A structural, empirical approach to scoring protein ligand complexes

C Springer et al.

JOURNAL OF MEDICINAL CHEMISTRY (2005)

Article Biochemistry & Molecular Biology

General and targeted statistical potentials for protein-ligand interactions

WTM Mooij et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Article Biochemical Research Methods

LigScore:: a novel scoring function for predicting binding affinities

A Krammer et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2005)

Article Chemistry, Medicinal

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)

Article Biochemistry & Molecular Biology

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)

Article Computer Science, Artificial Intelligence

Random forests

L Breiman

MACHINE LEARNING (2001)

Article Biochemistry & Molecular Biology

Knowledge-based scoring function to predict protein-ligand interactions

H Gohlke et al.

JOURNAL OF MOLECULAR BIOLOGY (2000)