A Comprehensive Review on Current Advances in Peptide Drug Development and Design

PBRpredict-Suite: a suite of models to predict peptide-recognition domain residues from protein sequence

(2018) Sumaiya Iqbal et al.   BIOINFORMATICS

Designing Peptidomimetics

(2018) Juan J. Perez   CURRENT TOPICS IN MEDICINAL CHEMISTRY

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

(2018) Pei Zhou et al.   NUCLEIC ACIDS RESEARCH

Cell penetrating peptides: A concise review with emphasis on biomedical applications

(2018) Hossein Derakhshankhah et al.   BIOMEDICINE & PHARMACOTHERAPY

Molecular Encapsulation Inside Microtubules Based on Tau-Derived Peptides

(2018) Hiroshi Inaba et al.   CHEMISTRY-A EUROPEAN JOURNAL

KELM-CPPpred: Kernel Extreme Learning Machine Based Prediction Model for Cell-Penetrating Peptides

(2018) Poonam Pandey et al.   JOURNAL OF PROTEOME RESEARCH

Peptide Nanomaterials Designed from Natural Supramolecular Systems

(2018) Hiroshi Inaba et al.   CHEMICAL RECORD

Short peptides interfering with signaling pathways as new therapeutic tools for cancer treatment

(2017) Aleksandra Ellert-Miklaszewska et al.   Future Medicinal Chemistry

CPPred-RF: A Sequence-based Predictor for Identifying Cell-Penetrating Peptides and Their Uptake Efficiency

(2017) Leyi Wei et al.   JOURNAL OF PROTEOME RESEARCH

Designed Tetrapeptide Interacts with Tubulin and Microtubule

(2017) Batakrishna Jana et al.   LANGMUIR

The pepATTRACT web server for blind, large-scale peptide–protein docking

(2017) Sjoerd J. de Vries et al.   NUCLEIC ACIDS RESEARCH

Cell permeability beyond the rule of 5

(2016) Pär Matsson et al.   ADVANCED DRUG DELIVERY REVIEWS

Discovery and Mechanism of Highly Efficient Cyclic Cell-Penetrating Peptides

(2016) Ziqing Qian et al.   BIOCHEMISTRY

Structure-based optimization of GRP78-binding peptides that enhances efficacy in cancer imaging and therapy

(2016) Sheng-Hung Wang et al.   BIOMATERIALS

Progress with peptide scanning to study structure-activity relationships: the implications for drug discovery

(2016) Stéphanie Eustache et al.   Expert Opinion on Drug Discovery

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

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

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Modulation of Protein–Protein Interactions for the Development of Novel Therapeutics

(2016) Ioanna Petta et al.   MOLECULAR THERAPY

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

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

Phage-displayed macrocyclic glycopeptide libraries

(2016) Simon Ng et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Lessons from (co-)evolution in the docking of proteins and peptides for CAPRI Rounds 28-35

(2016) Jinchao Yu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

(2016) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition

(2016) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Synergistic Anticancer Effect of Peptide-Docetaxel Nanoassembly Targeted to Tubulin: Toward Development of Dual Warhead Containing Nanomedicine

(2016) Saswat Mohapatra et al.   Advanced Healthcare Materials

Antimicrobial Peptides: An Emerging Category of Therapeutic Agents

(2016) Margit Mahlapuu et al.   Frontiers in Cellular and Infection Microbiology

Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes

(2015) Marta Pelay-Gimeno et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Minimalistic Predictor of Protein Binding Energy: Contribution of Solvation Factor to Protein Binding

(2015) Jeong-Mo Choi et al.   BIOPHYSICAL JOURNAL

A Web Interface for Easy Flexible Protein-Protein Docking with ATTRACT

(2015) Sjoerd J. de Vries et al.   BIOPHYSICAL JOURNAL

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

(2015) R. Rentzsch et al.   BRIEFINGS IN BIOINFORMATICS

Peptide Backbone Composition and Protease Susceptibility: Impact of Modification Type, Position, and Tandem Substitution

(2015) Halina M. Werner et al.   CHEMBIOCHEM

Peptide stapling techniques based on different macrocyclisation chemistries

(2015) Yu Heng Lau et al.   CHEMICAL SOCIETY REVIEWS

Protein Flexibility in Drug Discovery: From Theory to Computation

(2015) Rosa Buonfiglio et al.   ChemMedChem

Encoded libraries of chemically modified peptides

(2015) Christian Heinis et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Peptide therapeutics: current status and future directions

(2015) Keld Fosgerau et al.   DRUG DISCOVERY TODAY

Advances in phage display technology for drug discovery

(2015) Kobra Omidfar et al.   Expert Opinion on Drug Discovery

Cell-Permeable Cyclic Peptides from Synthetic Libraries Inspired by Natural Products

(2015) William M. Hewitt et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

CPPsite 2.0: a repository of experimentally validated cell-penetrating peptides

(2015) Piyush Agrawal et al.   NUCLEIC ACIDS RESEARCH

AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking

(2015) Avraham Ben-Shimon et al.   STRUCTURE

Discovery of a Direct Ras Inhibitor by Screening a Combinatorial Library of Cell-Permeable Bicyclic Peptides

(2015) Thi B. Trinh et al.   ACS Combinatorial Science

Strategic Approaches to Optimizing Peptide ADME Properties

(2014) Li Di   AAPS Journal

Cell-Penetrating Peptides: Design, Synthesis, and Applications

(2014) Dana Maria Copolovici et al.   ACS Nano

Early Endosomal Escape of a Cyclic Cell-Penetrating Peptide Allows Effective Cytosolic Cargo Delivery

(2014) Ziqing Qian et al.   BIOCHEMISTRY

Protein–protein binding affinity prediction from amino acid sequence

(2014) K. Yugandhar et al.   BIOINFORMATICS

ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli

(2014) F. Agostini et al.   BIOINFORMATICS

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

Peptides Containing β-Amino Acid Patterns: Challenges and Successes in Medicinal Chemistry

(2014) Chiara Cabrele et al.   JOURNAL OF MEDICINAL CHEMISTRY

Cell-Permeable Bicyclic Peptide Inhibitors against Intracellular Proteins

(2014) Wenlong Lian et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A rationally designed monomeric peptide triagonist corrects obesity and diabetes in rodents

(2014) Brian Finan et al.   NATURE MEDICINE

Feature selection and classification of protein-protein complexes based on their binding affinities using machine learning approaches

(2014) K. Yugandhar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Targeting CXCR4 with CTCE-9908 inhibits prostate tumor metastasis

(2014) Donald Wong et al.   BMC Urology

CPPpred: prediction of cell penetrating peptides

(2013) Thérèse A. Holton et al.   BIOINFORMATICS

A first-in-class, first-in-human, phase I trial of p28, a non-HDM2-mediated peptide inhibitor of p53 ubiquitination in patients with advanced solid tumours

(2013) M A Warso et al.   BRITISH JOURNAL OF CANCER

Cell penetrating peptides fail to induce an innate immune response in epithelial cells in vitro: Implications for continued therapeutic use

(2013) Edward Carter et al.   EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS

The Mitochondrial-Targeted Compound SS-31 Re-Energizes Ischemic Mitochondria by Interacting with Cardiolipin

(2013) A. V. Birk et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

In silico approaches for designing highly effective cell penetrating peptides

(2013) Ankur Gautam et al.   Journal of Translational Medicine

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

(2013) Mikael Trellet et al.   PLoS One

Stapled α−helical peptide drug development: A potent dual inhibitor of MDM2 and MDMX for p53-dependent cancer therapy

(2013) Yong S. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design of a Serum Stability Tag for Bioactive Peptides

(2013) Kalyani Jambunathan et al.   PROTEIN AND PEPTIDE LETTERS

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

N-Methylation of Peptides and Proteins: An Important Element for Modulating Biological Functions

(2012) Jayanta Chatterjee et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Protease-resistant peptide design-empowering nature's fragile warriors against HIV

(2012) Matthew T. Weinstock et al.   BIOPOLYMERS

PROSO II - a new method for protein solubility prediction

(2012) Pawel Smialowski et al.   FEBS Journal

PepSite: prediction of peptide-binding sites from protein surfaces

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

Specificity quantification of biomolecular recognition and its implication for drug discovery

(2012) Zhiqiang Yan et al.   Scientific Reports

PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors

(2011) E. Donsky et al.   BIOINFORMATICS

Peptides and Proteins as a Continuing Exciting Source of Inspiration for Peptidomimetics

(2011) Rob M. J. Liskamp et al.   CHEMBIOCHEM

New, Potent, Selective, and Short-Acting Peptidic V1aReceptor Agonists

(2011) Kazimierz Wiśniewski et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

(2011) Nir London et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Barak Raveh et al.   PLoS One

Secondary structure of cell-penetrating peptides controls membrane interaction and insertion

(2010) Emelía Eiríksdóttir et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Structure-based engineering of a monoclonal antibody for improved solubility

(2010) S.-J. Wu et al.   PROTEIN ENGINEERING DESIGN & SELECTION

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

Intrinsic amino acid side-chain hydrophilicity/hydrophobicity coefficients determined by reversed-phase high-performance liquid chromatography of model peptides: Comparison with other hydrophilicity/hydrophobicity scales

(2009) Colin T. Mant et al.   BIOPOLYMERS

PepX: a structural database of non-redundant protein–peptide complexes

(2009) Peter Vanhee et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Iris Antes   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accurate Prediction of Peptide Binding Sites on Protein Surfaces

(2009) Evangelia Petsalaki et al.   PLoS Computational Biology

Angiotensin-(1-7) with Thioether Bridge: An Angiotensin-Converting Enzyme-Resistant, Potent Angiotensin-(1-7) Analog

(2008) L. D. Kluskens et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

A CXCR4 Antagonist CTCE-9908 Inhibits Primary Tumor Growth and Metastasis of Breast Cancer

(2008) Eugene H. Huang et al.   JOURNAL OF SURGICAL RESEARCH

The exploration of macrocycles for drug discovery — an underexploited structural class

(2008) Edward M. Driggers et al.   NATURE REVIEWS DRUG DISCOVERY

Structure–activity relationships of Bak derived peptides: Affinity and specificity modulations by amino acid replacement

(2007) Virginie Frey et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY