Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking
出版年份 2016 全文链接
标题
Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking
作者
关键词
-
出版物
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
Volume 18, Issue 32, Pages 22129-22139
出版商
Royal Society of Chemistry (RSC)
发表日期
2016-07-14
DOI
10.1039/c6cp03670h
参考文献
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。- Evolution of protein interactions: From interactomes to interfaces
- (2014) Jessica Andreani et al. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
- ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers
- (2014) B. G. Pierce et al. BIOINFORMATICS
- Search strategies and evaluation in protein–protein docking: principles, advances and challenges
- (2014) Sheng-You Huang DRUG DISCOVERY TODAY
- Methods for analyzing and quantifying protein–protein interaction
- (2014) Syafrizayanti et al. Expert Review of Proteomics
- From workstations to workbenches: Towards predicting physicochemically viable protein-protein interactions across a host and a pathogen
- (2014) Gayatri Ramakrishnan et al. IUBMB LIFE
- Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set
- (2014) Huiyong Sun et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring
- (2014) Huiyong Sun et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- DrugScorePPI Knowledge-Based Potentials Used as Scoring and Objective Function in Protein-Protein Docking
- (2014) Dennis M. Krüger et al. PLoS One
- Protein-Protein Interactions and Prediction: A Comprehensive Overview
- (2014) Gopichandran Sowmya et al. PROTEIN AND PEPTIDE LETTERS
- Specificity and affinity quantification of protein-protein interactions
- (2013) Z. Yan et al. BIOINFORMATICS
- Protein–protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches
- (2013) Armand G. Ngounou Wetie et al. CELLULAR AND MOLECULAR LIFE SCIENCES
- Hot-Spot Mapping of the Interactions between Chymosin and Bovine κ-Casein
- (2013) Jesper Sørensen et al. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
- Molecular Determinants of Binding to the Plasmodium Subtilisin-like Protease 1
- (2013) Simone Fulle et al. Journal of Chemical Information and Modeling
- MMGBSA As a Tool To Understand the Binding Affinities of Filamin–Peptide Interactions
- (2013) Mikko Ylilauri et al. Journal of Chemical Information and Modeling
- Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models
- (2013) Lei Xu et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Protein-Protein Docking with F2Dock 2.0 and GB-Rerank
- (2013) Rezaul Chowdhury et al. PLoS One
- Improving ranking of models for protein complexes with side chain modeling and atomic potentials
- (2013) Shruthi Viswanath et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Protein models: The Grand Challenge of protein docking
- (2013) Ivan Anishchenko et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Modulating Protein-Protein Interactions: From Structural Determinants of Binding to Druggability Prediction to Application
- (2012) Alexander Metz et al. CURRENT PHARMACEUTICAL DESIGN
- Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation
- (2012) Kazuhiro Takemura et al. JOURNAL OF CHEMICAL PHYSICS
- On the binding affinity of macromolecular interactions: daring to ask why proteins interact
- (2012) P. L. Kastritis et al. Journal of the Royal Society Interface
- Microscale thermophoresis quantifies biomolecular interactions under previously challenging conditions
- (2012) Susanne A.I. Seidel et al. METHODS
- Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method
- (2012) Nadine Homeyer et al. Molecular Informatics
- Prediction of protein-protein binding free energies
- (2012) Thom Vreven et al. PROTEIN SCIENCE
- Biophysical and computational fragment-based approaches to targeting protein–protein interactions: applications in structure-guided drug discovery
- (2012) Anja Winter et al. QUARTERLY REVIEWS OF BIOPHYSICS
- COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes
- (2011) A. Vangone et al. BIOINFORMATICS
- Structure-based computational analysis of protein binding sites for function and druggability prediction
- (2011) Britta Nisius et al. JOURNAL OF BIOTECHNOLOGY
- Applications of isothermal titration calorimetry in pure and applied research-survey of the literature from 2010
- (2011) Rajesh Ghai et al. JOURNAL OF MOLECULAR RECOGNITION
- Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library
- (2011) Brian G. Pierce et al. PLoS One
- Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations
- (2010) Tingjun Hou et al. Journal of Chemical Information and Modeling
- Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking
- (2010) Tingjun Hou et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark
- (2010) Panagiotis L. Kastritis et al. JOURNAL OF PROTEOME RESEARCH
- Are Scoring Functions in Protein−Protein Docking Ready to Predict Interactomes? Clues from a Novel Binding Affinity Benchmark
- (2010) Panagiotis L. Kastritis et al. JOURNAL OF PROTEOME RESEARCH
- 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
- Comparing experimental and computational alanine scanning techniques for probing a prototypical protein–protein interaction
- (2010) Richard T. Bradshaw et al. PROTEIN ENGINEERING DESIGN & SELECTION
- Protein-protein docking benchmark version 4.0
- (2010) Howook Hwang et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Designing coarse grained-and atom based-potentials for protein-protein docking
- (2010) Dror Tobi BMC STRUCTURAL BIOLOGY
- Identification of structural determinants for inhibition strength and specificity of wheat xylanase inhibitors TAXI-IA and TAXI-IIA
- (2009) Annick Pollet et al. FEBS Journal
- DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking
- (2008) Gwo-Yu Chuang et al. BIOPHYSICAL JOURNAL
- Predicting 3D Structures of Protein-Protein Complexes
- (2008) Ilya Vakser et al. CURRENT PHARMACEUTICAL BIOTECHNOLOGY
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started