Predicting Protein–Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment

InterPep2: global peptide–protein docking using interaction surface templates

(2020) Isak Johansson-Åkhe et al.   BIOINFORMATICS

AutoDock CrankPep: combining folding and docking to predict protein–peptide complexes

(2019) Yuqi Zhang et al.   BIOINFORMATICS

PepPro: A Nonredundant Structure Data Set for Benchmarking Peptide–Protein Computational Docking

(2019) Xianjin Xu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition

(2019) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Interfering peptides targeting protein–protein interactions: the next generation of drugs?

(2018) Heriberto Bruzzoni-Giovanelli et al.   DRUG DISCOVERY TODAY

Protein–peptide docking: opportunities and challenges

(2018) Maciej Ciemny et al.   DRUG DISCOVERY TODAY

Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides

(2018) Pei Zhou et al.   Journal of Chemical Information and Modeling

HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm

(2018) Pei Zhou et al.   NUCLEIC ACIDS RESEARCH

FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility

(2017) Orly Marcu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock

(2017) Nawsad Alam et al.   PLoS Computational Biology

LEADS-PEP: A Benchmark Data Set for Assessment of Peptide Docking Performance

(2016) Alexander Sebastian Hauser et al.   Journal of Chemical Information and Modeling

PepComposer: computational design of peptides binding to a given protein surface

(2016) Agnieszka Obarska-Kosinska et al.   NUCLEIC ACIDS RESEARCH

Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction

(2016) Chengfei Yan et al.   STRUCTURE

PCalign: a method to quantify physicochemical similarity of protein-protein interfaces

(2015) Shanshan Cheng et al.   BMC BIOINFORMATICS

Peptide therapeutics: current status and future directions

(2015) Keld Fosgerau et al.   DRUG DISCOVERY TODAY

GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization

(2015) Hasup Lee et al.   NUCLEIC ACIDS RESEARCH

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

(2015) Mateusz Kurcinski et al.   NUCLEIC ACIDS RESEARCH

Fully Blind Peptide-Protein Docking with pepATTRACT

(2015) Christina E.M. Schindler et al.   STRUCTURE

AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking

(2015) Avraham Ben-Shimon et al.   STRUCTURE

Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how

(2013) Nir London et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein-Peptide Complex Prediction through Fragment Interaction Patterns

(2013) Erik Verschueren et al.   STRUCTURE

Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions

(2011) Nir London et al.   NUCLEIC ACIDS RESEARCH

Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

(2011) Brian G. Pierce et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The Structural Basis of Peptide-Protein Binding Strategies

(2010) Nir London et al.   STRUCTURE

Linking folding and binding

(2009) Peter E Wright et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility

(2009) Iris Antes   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-Peptide Interactions Adopt the Same Structural Motifs as Monomeric Protein Folds

(2009) Peter Vanhee et al.   STRUCTURE

Peptide-mediated interactions in biological systems: new discoveries and applications

(2008) Evangelia Petsalaki et al.   CURRENT OPINION IN BIOTECHNOLOGY

An iterative knowledge-based scoring function for protein-protein recognition

(2008) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS