- Home
- Publications
- Publication Search
- Publication Details
Title
Protein flexibility in docking and surface mapping
Authors
Keywords
-
Journal
QUARTERLY REVIEWS OF BIOPHYSICS
Volume 45, Issue 03, Pages 301-343
Publisher
Cambridge University Press (CUP)
Online
2012-05-09
DOI
10.1017/s0033583512000066
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Accounting for Induced-Fit Effects in Docking: What is Possible and What is Not?
- (2012) Christoph A. Sotriffer CURRENT TOPICS IN MEDICINAL CHEMISTRY
- Protein-ligand docking
- (2011) Giovanni Bottegoni Frontiers in Bioscience-Landmark
- Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations
- (2011) E. Prabhu Raman et al. Journal of Chemical Information and Modeling
- CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes
- (2011) James B. Dunbar et al. Journal of Chemical Information and Modeling
- CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions
- (2011) Richard D. Smith et al. Journal of Chemical Information and Modeling
- Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening
- (2011) Sara E. Nichols et al. Journal of Chemical Information and Modeling
- Computer-aided drug-discovery techniques that account for receptor flexibility
- (2010) Jacob D Durrant et al. CURRENT OPINION IN PHARMACOLOGY
- Successful Applications of Computer Aided Drug Discovery: Moving Drugs from Concept to the Clinic
- (2010) Tanaji Talele et al. CURRENT TOPICS IN MEDICINAL CHEMISTRY
- Role of protein flexibility in the discovery of new drugs
- (2010) Gloria Fuentes et al. DRUG DEVELOPMENT RESEARCH
- How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis
- (2010) Olivier Sperandio et al. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
- Docking Validation Resources: Protein Family and Ligand Flexibility Experiments
- (2010) Sudipto Mukherjee et al. Journal of Chemical Information and Modeling
- Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments
- (2010) Ian R. Craig et al. Journal of Chemical Information and Modeling
- Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
- (2010) Dariusz Plewczynski et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Relaxed complex scheme suggests novel inhibitors for the lyase activity of DNA polymerase beta
- (2010) Khaled Barakat et al. JOURNAL OF MOLECULAR GRAPHICS & MODELLING
- Full Protein Flexibility Is Essential for Proper Hot-Spot Mapping
- (2010) Katrina W. Lexa et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding
- (2010) Angela M. Henzler et al. Molecular Informatics
- 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
- Folding and binding cascades: Dynamic landscapes and population shifts
- (2010) Sandeep Kumar et al. PROTEIN SCIENCE
- Mining protein dynamics from sets of crystal structures using “consensus structures”
- (2010) Gerard J. P. van Westen et al. PROTEIN SCIENCE
- Computational Analysis of Protein Hotspots
- (2010) Chao-Yie Yang et al. ACS Medicinal Chemistry Letters
- Computational Identification of Uncharacterized Cruzain Binding Sites
- (2010) Jacob D. Durrant et al. PLoS Neglected Tropical Diseases
- Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques
- (2009) Ryan Brenke et al. BIOINFORMATICS
- A virtual screening study of the acetylcholine binding protein using a relaxed–complex approach
- (2009) Arneh Babakhani et al. COMPUTATIONAL BIOLOGY AND CHEMISTRY
- Managing protein flexibility in docking and its applications
- (2009) Chandrika B-Rao et al. DRUG DISCOVERY TODAY
- Grand Canonical Free-Energy Calculations of Protein−Ligand Binding
- (2009) Matthew Clark et al. Journal of Chemical Information and Modeling
- Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs
- (2009) Christopher R. Corbeil et al. Journal of Chemical Information and Modeling
- Docking Ligands into Flexible and Solvated Macromolecules. 4. Are Popular Scoring Functions Accurate for this Class of Proteins?
- (2009) Pablo Englebienne et al. Journal of Chemical Information and Modeling
- Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes
- (2009) Manuel Rueda et al. Journal of Chemical Information and Modeling
- Recipes for the Selection of Experimental Protein Conformations for Virtual Screening
- (2009) Manuel Rueda et al. Journal of Chemical Information and Modeling
- Docking Ligands on Protein Surfaces: The Case Study of Prion Protein‡
- (2009) Agata Kranjc et al. Journal of Chemical Theory and Computation
- AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
- (2009) Garrett M. Morris et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design
- (2009) Christian R. Schubert et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation
- (2009) Ajay N. Jain JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Binding Site Detection and Druggability Index from First Principles
- (2009) Jesus Seco et al. JOURNAL OF MEDICINAL CHEMISTRY
- Ensemble-based virtual screening reveals dual-inhibitors for the p53–MDM2/MDMX interactions
- (2009) Khaled Barakat et al. JOURNAL OF MOLECULAR GRAPHICS & MODELLING
- Docking Flexible Peptide to Flexible Protein by Molecular Dynamics Using Two Implicit-Solvent Models: An Evaluation in Protein Kinase and Phosphatase Systems
- (2009) Zunnan Huang et al. JOURNAL OF PHYSICAL CHEMISTRY B
- The rise of fragment-based drug discovery
- (2009) Christopher W. Murray et al. Nature Chemistry
- Conformational selection or induced fit: A flux description of reaction mechanism
- (2009) G. G. Hammes et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Blind docking of pharmaceutically relevant compounds using RosettaLigand
- (2009) Ian W. Davis et al. PROTEIN SCIENCE
- Multiple solvent crystal structures of ribonuclease A: An assessment of the method
- (2009) Michelle Dechene et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
- (2009) David L. Mobley et al. STRUCTURE
- Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation
- (2009) Olgun Guvench et al. PLoS Computational Biology
- A poke in the eye: Inhibiting HIV-1 protease through its flap-recognition pocket
- (2008) Kelly L. Damm et al. BIOPOLYMERS
- AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening
- (2008) Tania Pencheva et al. BMC BIOINFORMATICS
- Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble
- (2008) Melissa R. Landon et al. Chemical Biology & Drug Design
- How to Efficiently Include Receptor Flexibility During Computational Docking
- (2008) Andreas May et al. Current Computer-Aided Drug Design
- Flexible ligand docking to multiple receptor conformations: a practical alternative
- (2008) Maxim Totrov et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Docking Ligands into Flexible and Solvated Macromolecules. 2. Development and Application of Fitted1.5 to the Virtual Screening of Potential HCV Polymerase Inhibitors
- (2008) Christopher R. Corbeil et al. Journal of Chemical Information and Modeling
- Protein−Ligand Docking against Non-Native Protein Conformers
- (2008) Marcel L. Verdonk et al. Journal of Chemical Information and Modeling
- Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange
- (2008) Martin Zacharias Journal of Chemical Theory and Computation
- A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
- (2008) Giovanni Bottegoni et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
- (2008) Rommie E. Amaro et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase
- (2008) Lily S. Cheng et al. JOURNAL OF MEDICINAL CHEMISTRY
- Design of Annulated Pyrazoles as Inhibitors of HIV-1 Reverse Transcriptase∥
- (2008) Zachary K. Sweeney et al. JOURNAL OF MEDICINAL CHEMISTRY
- Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking
- (2008) Andreas May et al. JOURNAL OF MEDICINAL CHEMISTRY
- Target Flexibility: An Emerging Consideration in Drug Discovery and Design†
- (2008) Pietro Cozzini et al. JOURNAL OF MEDICINAL CHEMISTRY
- Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking
- (2008) Giovanni Bottegoni et al. JOURNAL OF MEDICINAL CHEMISTRY
- Fragment-Based Discovery of the Pyrazol-4-yl Urea (AT9283), a Multitargeted Kinase Inhibitor with Potent Aurora Kinase Activity†
- (2008) Steven Howard et al. JOURNAL OF MEDICINAL CHEMISTRY
- RosettaLigand Docking with Full Ligand and Receptor Flexibility
- (2008) Ian W. Davis et al. JOURNAL OF MOLECULAR BIOLOGY
- Current topics in computer‐aided drug design
- (2008) Carlton A. Taft et al. JOURNAL OF PHARMACEUTICAL SCIENCES
- Prediction of Cytochrome P450 2B6-Substrate Interactions Using Pharmacophore Ensemble/Support Vector Machine (PhE/SVM) Approach
- (2008) Max Leong et al. Medicinal Chemistry
- Development of a New Predictive Model for Interactions with Human Cytochrome P450 2A6 Using Pharmacophore Ensemble/Support Vector Machine (PhE/SVM) Approach
- (2008) Max K. Leong et al. PHARMACEUTICAL RESEARCH
- Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection
- (2008) S. M. Sullivan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Solvent dramatically affects protein structure refinement
- (2008) G. Chopra et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Selected-fit versus induced-fit protein binding: Kinetic differences and mutational analysis
- (2008) Thomas R. Weikl et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- In pursuit of virtual lead optimization: Pruning ensembles of receptor structures for increased efficiency and accuracy during docking
- (2008) Erin S. D. Bolstad et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking
- (2008) Erin S. D. Bolstad et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- COCO: A simple tool to enrich the representation of conformational variability in NMR structures
- (2008) Charles A. Laughton et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go
- (2007) N Moitessier et al. BRITISH JOURNAL OF PHARMACOLOGY
- Modeling and Selection of Flexible Proteins for Structure-Based Drug Design: Backbone and Side Chain Movements in p38 MAPK
- (2007) Jyothi Subramanian et al. ChemMedChem
- Conformational selectionin silico: Loop latching motions and ligand binding in enzymes
- (2007) Sergio Wong et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now