Docking small peptides remains a great challenge: an assessment using AutoDock Vina

PeptiSite: A structural database of peptide binding sites in 4D

(2014) Chayan Acharya et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Rapid Flow-Based Peptide Synthesis

(2014) Mark D. Simon et al.   CHEMBIOCHEM

Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation

(2014) Kim Van Roey et al.   CHEMICAL REVIEWS

PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces

(2014) Adrien Saladin et al.   NUCLEIC ACIDS RESEARCH

Identification of Urinary Peptide Biomarkers Associated with Rheumatoid Arthritis

(2014) Angelique Stalmach et al.   PLoS One

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

(2014) Sergio Ruiz-Carmona et al.   PLoS Computational Biology

Oligopeptides as Biomarkers of Cyanobacterial Subpopulations. Toward an Understanding of Their Biological Role

(2014) Ramsy Agha et al.   Toxins

Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field

(2013) S.F. Sousa et al.   CURRENT MEDICINAL CHEMISTRY

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

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

The Role of Protonation States in Ligand-Receptor Recognition and Binding

(2013) Marharyta Petukh et al.   CURRENT PHARMACEUTICAL DESIGN

A de novo-designed antimicrobial peptide with activity against multiresistant Staphylococcus aureus acting on RsbW kinase

(2013) Alexandra Dangel et al.   FASEB JOURNAL

Approaches for enhancing oral bioavailability of peptides and proteins

(2013) Jwala Renukuntla et al.   INTERNATIONAL JOURNAL OF PHARMACEUTICS

Improved Docking of Polypeptides with Glide

(2013) Ivan Tubert-Brohman et al.   Journal of Chemical Information and Modeling

Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise

(2013) David Ryan Koes et al.   Journal of Chemical Information and Modeling

Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines

(2013) Xiaohua Zhang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AutoGrow 3.0: An improved algorithm for chemically tractable, semi-automated protein inhibitor design

(2013) Jacob D. Durrant et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Antimicrobial peptides stage a comeback

(2013) Jeffrey L Fox   NATURE BIOTECHNOLOGY

Inhibition of α-helix-mediated protein–protein interactions using designed molecules

(2013) Valeria Azzarito et al.   Nature Chemistry

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking

(2013) Mikael Trellet et al.   PLoS One

Towards Ligand Docking Including Explicit Interface Water Molecules

(2013) Gordon Lemmon et al.   PLoS One

Detection of peptide-binding sites on protein surfaces: The first step toward the modeling and targeting of peptide-mediated interactions

(2013) Assaf Lavi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-Peptide Complex Prediction through Fragment Interaction Patterns

(2013) Erik Verschueren et al.   STRUCTURE

DINC: A new AutoDock-based protocol for docking large ligands

(2013) Ankur Dhanik et al.   BMC STRUCTURAL BIOLOGY

PeptideBuilder: A simple Python library to generate model peptides

(2013) Matthew Z. Tien et al.   PeerJ

PepBind: A Comprehensive Database and Computational Tool for Analysis of Protein–peptide Interactions

(2013) Arindam Atanu Das et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Advances in the Prediction of Protein-Peptide Binding Affinities: Implications for Peptide-Based Drug Discovery

(2012) Joseph Audie et al.   Chemical Biology & Drug Design

The Future of Peptide-based Drugs

(2012) David J. Craik et al.   Chemical Biology & Drug Design

Recent work in the development and application of protein–peptide docking

(2012) Joseph Audie et al.   Future Medicinal Chemistry

QuickVina: Accelerating AutoDock Vina Using Gradient-Based Heuristics for Global Optimization

(2012) Stephanus Daniel Handoko et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Variability in docking success rates due to dataset preparation

(2012) Christopher R. Corbeil et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

PepSite: prediction of peptide-binding sites from protein surfaces

(2012) L. G. Trabuco et al.   NUCLEIC ACIDS RESEARCH

Peptide Array X-Linking (PAX): A New Peptide-Protein Identification Approach

(2012) Hirokazu Okada et al.   PLoS One

Accessible High-Throughput Virtual Screening Molecular Docking Software for Students and Educators

(2012) Reed B. Jacob et al.   PLoS Computational Biology

In vitro methods for peptide display and their applications

(2011) C. G. Ullman et al.   Briefings in Functional Genomics

Studying protein–protein interactions using peptide arrays

(2011) Chen Katz et al.   CHEMICAL SOCIETY REVIEWS

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

(2011) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

(2011) Barak Raveh et al.   PLoS One

Toward prediction of functional protein pockets using blind docking and pocket search algorithms

(2011) Csaba Hetényi et al.   PROTEIN SCIENCE

Structural and Dynamic Determinants of Protein-Peptide Recognition

(2011) Onur Dagliyan et al.   STRUCTURE

VitAL: Viterbi Algorithm for de novo Peptide Design

(2010) E. Besray Unal et al.   PLoS One

Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina

(2010) Max W. Chang et al.   PLoS One

Sub-angstrom modeling of complexes between flexible peptides and globular proteins

(2010) Barak Raveh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Structural Basis of Peptide-Protein Binding Strategies

(2010) Nir London et al.   STRUCTURE

Re-refinement from deposited X-ray data can deliver improved models for most PDB entries

(2009) Robbie P. Joosten et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Inhibition of protein–protein interactions using designed molecules

(2009) Andrew J. Wilson   CHEMICAL SOCIETY REVIEWS

Toward the fast blind docking of a peptide to a target protein by using a four-body statistical pseudo-potential

(2009) Takuyo Aita et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Synthetic therapeutic peptides: science and market

(2009) Patrick Vlieghe et al.   DRUG DISCOVERY TODAY

Effect of Input Differences on the Results of Docking Calculations

(2009) Miklos Feher et al.   Journal of Chemical Information and Modeling

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

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

MetaPocket: A Meta Approach to Improve Protein Ligand Binding Site Prediction

(2009) Bingding Huang   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

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

(2009) Iris Antes   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling

(2008) P. Arun Prasad et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Efficient docking of peptides to proteins without prior knowledge of the binding site

(2002) Csaba Hetényi et al.   PROTEIN SCIENCE