Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana

CLE peptides and their signaling pathways in plant development

(2016) Yasuka L. Yamaguchi et al.   JOURNAL OF EXPERIMENTAL BOTANY

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Small-Molecule and Peptide Inhibitors of the Pro-Survival Protein Mcl-1

(2015) Andrew M. Beekman et al.   ChemMedChem

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

Exploring the Secrets of Long Noncoding RNAs

(2015) Mingyang Quan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the Binding Protein: Troponin I Fragment–Troponin C System

(2015) Jacek Wabik et al.   MOLECULES

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

PLIP: fully automated protein–ligand interaction profiler

(2015) Sebastian Salentin et al.   NUCLEIC ACIDS RESEARCH

The Plant Peptidome: An Expanding Repertoire of Structural Features and Biological Functions

(2015) Patrizia Tavormina et al.   PLANT CELL

Fully Blind Peptide-Protein Docking with pepATTRACT

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

Tools and Strategies to Match Peptide-Ligand Receptor Pairs

(2014) M. A. Butenko et al.   PLANT CELL

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs

(2013) Jeroen Crappé et al.   BMC GENOMICS

Druggable protein–protein interactions – from hot spots to hot segments

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

Mining the genome of Arabidopsis thaliana as a basis for the identification of novel bioactive peptides involved in oxidative stress tolerance

(2013) Barbara De Coninck et al.   JOURNAL OF EXPERIMENTAL BOTANY

GalaxyRefine: protein structure refinement driven by side-chain repacking

(2013) Lim Heo et al.   NUCLEIC ACIDS RESEARCH

PDBe: Protein Data Bank in Europe

(2013) Aleksandras Gutmanas et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Mikael Trellet et al.   PLoS One

Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening

(2013) Arnab Bhattacherjee et al.   PLoS Computational Biology

PeptideBuilder: A simple Python library to generate model peptides

(2013) Matthew Z. Tien et al.   PeerJ

GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions

(2012) Junsu Ko et al.   BMC BIOINFORMATICS

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

(2012) Sameer Velankar et al.   NUCLEIC ACIDS RESEARCH

PepSite: prediction of peptide-binding sites from protein surfaces

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

Small Signaling Peptides in Arabidopsis Development: How Cells Communicate Over a Short Distance

(2012) E. Murphy et al.   PLANT CELL

“And yet it moves”: Cell-to-cell and long-distance signaling by plant microRNAs

(2012) Esther Marín-González et al.   PLANT SCIENCE

The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation

(2012) M. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BINANA: A novel algorithm for ligand-binding characterization

(2011) Jacob D. Durrant et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

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

(2011) Barak Raveh et al.   PLoS One

Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase

(2011) D. Cardinale et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hundreds of putatively functional small open reading frames in Drosophila

(2011) Emmanuel Ladoukakis et al.   GENOME BIOLOGY

Lilliputians get into the limelight: Novel class of small peptide genes in morphogenesis

(2010) Yoshiko Hashimoto et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

The march of the PINs: developmental plasticity by dynamic polar targeting in plant cells

(2010) Wim Grunewald et al.   EMBO JOURNAL

Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands

(2010) Feng Ding et al.   Journal of Chemical Information and Modeling

Post-Translational Modifications in Secreted Peptide Hormones in Plants

(2010) Y. Matsubayashi   PLANT AND CELL PHYSIOLOGY

The Structural Basis of Peptide-Protein Binding Strategies

(2010) Nir London et al.   STRUCTURE

Transient Protein-Protein Interactions: Structural, Functional, and Network Properties

(2010) James R. Perkins et al.   STRUCTURE

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

Convergence and combination of methods in protein–protein docking

(2009) Sandor Vajda et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses

(2008) B. Ben Amor et al.   GENOME RESEARCH

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Contextual Specificity in Peptide-Mediated Protein Interactions

(2008) Amelie Stein et al.   PLoS One

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation