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Title
Protein–Protein Docking: Past, Present, and Future
Authors
Keywords
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Journal
PROTEIN JOURNAL
Volume 41, Issue 1, Pages 1-26
Publisher
Springer Science and Business Media LLC
Online
2021-11-17
DOI
10.1007/s10930-021-10031-8
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- (2021) Hana Štorkánová et al. Scientific Reports
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- (2021) Lucas S. P. Rudden et al. Journal of Chemical Information and Modeling
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- (2021) Johnathan D. Guest et al. STRUCTURE
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- (2021) Sharon Sunny et al. COMPUTATIONAL BIOLOGY AND CHEMISTRY
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- (2021) Gennady M. Verkhivker et al. JOURNAL OF PHYSICAL CHEMISTRY B
- LZerD webserver for pairwise and multiple protein–protein docking
- (2021) Charles Christoffer et al. NUCLEIC ACIDS RESEARCH
- Highly accurate protein structure prediction with AlphaFold
- (2021) John Jumper et al. NATURE
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- (2021) Minkyung Baek et al. SCIENCE
- Prediction of Protein–Protein Interaction Sites Using Convolutional Neural Network and Improved Data Sets
- (2020) Zengyan Xie et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Fundamentals of Recurrent Neural Network (RNN) and Long Short-Term Memory (LSTM) network
- (2020) Alex Sherstinsky PHYSICA D-NONLINEAR PHENOMENA
- Challenges and opportunities of automated protein‐protein docking: HDOCK server vs human predictions in CAPRI Rounds 38‐46
- (2020) Yumeng Yan et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Energy‐based Graph Convolutional Networks for Scoring Protein Docking Models
- (2020) Yue Cao et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Mol-CycleGAN: a generative model for molecular optimization
- (2020) Łukasz Maziarka et al. Journal of Cheminformatics
- Combining Spectral Unmixing and 3D/2D Dense Networks with Early-Exiting Strategy for Hyperspectral Image Classification
- (2020) Bei Fang et al. Remote Sensing
- Prediction of protein–protein complexes using replica exchange with repulsive scaling
- (2020) Till Siebenmorgen et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
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- (2020) Maria Elisa Ruiz Echartea et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations
- (2020) Paweł Krupa et al. BIOINFORMATICS
- Generative adversarial networks
- (2020) Ian Goodfellow et al. COMMUNICATIONS OF THE ACM
- Atomic-resolution protein structure determination by cryo-EM
- (2020) Ka Man Yip et al. NATURE
- Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination
- (2020) Ryan E. Pavlovicz et al. PLoS Computational Biology
- ‘It will change everything’: DeepMind’s AI makes gigantic leap in solving protein structures
- (2020) Ewen Callaway NATURE
- Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes
- (2020) Stephan Eismann et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Integrative modeling of membrane-associated protein assemblies
- (2020) Jorge Roel-Touris et al. Nature Communications
- Advances to tackle backbone flexibility in protein docking
- (2020) Ameya Harmalkar et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- EROS-DOCK: Protein-Protein Docking Using Exhaustive Branch-and-Bound Rotational Search
- (2019) Maria Elisa Echartea Ruiz et al. BIOINFORMATICS
- Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein–protein interactions
- (2019) Ankit A Roy et al. NUCLEIC ACIDS RESEARCH
- Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space
- (2019) Matteo T. Degiacomi STRUCTURE
- iScore: A novel graph kernel-based function for scoring protein-protein docking models
- (2019) Cunliang Geng et al. BIOINFORMATICS
- LightDock goes information-driven
- (2019) Jorge Roel-Touris et al. BIOINFORMATICS
- Less is more: Coarse-grained integrative modeling of large biomolecular assemblies with HADDOCK
- (2019) Jorge Roel-Touris et al. Journal of Chemical Theory and Computation
- Protein Docking Using a Single Representation for Protein Surface, Electrostatics, and Local Dynamics
- (2019) Lucas S. P. Rudden et al. Journal of Chemical Theory and Computation
- Sequence-based prediction of protein-protein interaction sites by simplified long short-term memory network
- (2019) Buzhong Zhang et al. NEUROCOMPUTING
- Protein Docking Model Evaluation by 3D Deep Convolutional Neural Networks
- (2019) Xiao Wang et al. BIOINFORMATICS
- ConvsPPIS: Identifying Protein-protein Interaction Sites by an Ensemble Convolutional Neural Network with Feature Graph
- (2019) Huaixu Zhu et al. Current Bioinformatics
- MathDL: mathematical deep learning for D3R Grand Challenge 4
- (2019) Duc Duy Nguyen et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
- (2019) Marc F. Lensink et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
- (2019) P. Gainza et al. NATURE METHODS
- OUP accepted manuscript
- (2018) BIOINFORMATICS
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- (2018) Ruben Sanchez-Garcia et al. BIOINFORMATICS
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- (2018) Lukas Zimmermann et al. JOURNAL OF MOLECULAR BIOLOGY
- InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs
- (2018) Chloé Quignot et al. NUCLEIC ACIDS RESEARCH
- Protein–protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique
- (2018) Xiaoying Wang et al. BIOINFORMATICS
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- (2017) Minkyung Baek et al. NUCLEIC ACIDS RESEARCH
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- (2017) Petras J. Kundrotas et al. PROTEIN SCIENCE
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- (2016) P. B. Jayaraj et al. Journal of Cheminformatics
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- (2015) Florian Krull et al. Journal of Chemical Information and Modeling
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- (2015) Alessia David et al. JOURNAL OF MOLECULAR BIOLOGY
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- (2015) Eduard Porta-Pardo et al. PLoS Computational Biology
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- (2015) Zhe Zhang et al. PLoS One
- CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts
- (2014) E. Chermak et al. BIOINFORMATICS
- MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers
- (2014) Masahito Ohue et al. BIOINFORMATICS
- Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions
- (2014) Engin Cukuroglu et al. PLoS One
- InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution
- (2013) Jessica Andreani et al. BIOINFORMATICS
- pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring
- (2013) Brian Jiménez-García et al. BIOINFORMATICS
- SP-Dock: Protein-Protein Docking Using Shape and Physicochemical Complementarity
- (2013) A. Axenopoulos et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- CABS-fold: server for the de novo and consensus-based prediction of protein structure
- (2013) Maciej Blaszczyk et al. NUCLEIC ACIDS RESEARCH
- CABS-flex: server for fast simulation of protein structure fluctuations
- (2013) Michal Jamroz et al. NUCLEIC ACIDS RESEARCH
- Replica Exchange Improves Sampling in Low-Resolution Docking Stage of RosettaDock
- (2013) Zhe Zhang et al. PLoS One
- Blind prediction of interfacial water positions in CAPRI
- (2013) Marc F. Lensink et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions
- (2013) Rocco Moretti et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Intuitive, but not simple: Including explicit water molecules in protein-protein docking simulations improves model quality
- (2013) Hardik I. Parikh et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Docking, scoring, and affinity prediction in CAPRI
- (2013) Marc F. Lensink et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- PAIRpred: Partner-specific prediction of interacting residues from sequence and structure
- (2013) Fayyaz ul Amir Afsar Minhas et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling
- (2013) Matteo T. Degiacomi et al. STRUCTURE
- Cell-Dock: high-performance protein–protein docking
- (2012) Carles Pons et al. BIOINFORMATICS
- CD-HIT: accelerated for clustering the next-generation sequencing data
- (2012) Limin Fu et al. BIOINFORMATICS
- AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing
- (2012) Aram Davtyan et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Predictive energy landscapes for protein-protein association
- (2012) W. Zheng et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A Shape Descriptor for Fast Complementarity Matching in Molecular Docking
- (2011) A. Axenopoulos et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- SDOCK: A global protein-protein docking program using stepwise force-field potentials
- (2011) Changsheng Zhang et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology
- (2011) Sarel J. Fleishman et al. JOURNAL OF MOLECULAR BIOLOGY
- HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
- (2011) Michael Remmert et al. NATURE METHODS
- New measures for estimating surface complementarity and packing at protein-protein interfaces
- (2010) Pralay Mitra et al. FEBS LETTERS
- SwarmDock and the Use of Normal Modes in Protein-Protein Docking
- (2010) Iain H. Moal et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Protein-protein docking benchmark version 4.0
- (2010) Howook Hwang et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Protein-protein docking using region-based 3D Zernike descriptors
- (2009) Vishwesh Venkatraman et al. BMC BIOINFORMATICS
- Crystal contacts as nature's docking solutions
- (2009) Evgeny Krissinel JOURNAL OF COMPUTATIONAL CHEMISTRY
- Target Flexibility: An Emerging Consideration in Drug Discovery and Design†
- (2008) Pietro Cozzini et al. JOURNAL OF MEDICINAL CHEMISTRY
- The RosettaDock server for local protein-protein docking
- (2008) S. Lyskov et al. NUCLEIC ACIDS RESEARCH
- An iterative knowledge-based scoring function for protein-protein recognition
- (2008) Sheng-You Huang et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Specific interactions for ab initio folding of protein terminal regions with secondary structures
- (2008) Yuedong Yang et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Protein-protein docking benchmark version 3.0
- (2008) Howook Hwang et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Defining and characterizing protein surface using alpha shapes
- (2008) Laurent-Philippe Albou et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
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