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

https://doi.org/10.1002/prot.22629
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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New general approach for determining the solution structure of a ligand bound weakly to a receptor: structure of a fibrinogen A?-like peptide bound to thrombin(S195A) obtained using NOE distance constraints and an ECEPP/3 flexible docking program
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Generalized-ensemble algorithms for molecular simulations of biopolymers
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Gaussian docking functions
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FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function
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Detailed analysis of grid‐based molecular docking: A case study of CDOCKER—A CHARMm‐based MD docking algorithm
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AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high‐resolution modeling
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Inhibition of LFA‐1/ICAM‐1 and VLA‐4/VCAM‐1 as a therapeutic approach to inflammation and autoimmune diseases
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Combining docking and molecular dynamic simulations in drug design
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Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
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ICM‐DISCO docking by global energy optimization with fully flexible side‐chains
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Predicting peptide binding to MHC pockets via molecular modeling, implicit solvation, and global optimization
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A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
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Comparative evaluation of eight docking tools for docking and virtual screening accuracy
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Ab initio prediction of peptide‐MHC binding geometry for diverse class I MHC allotypes
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Protein–ligand docking: Current status and future challenges
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Flexible protein–flexible ligand docking with disrupted velocity simulated annealing
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Docking and scoring with alternative side‐chain conformations
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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FlexE: efficient molecular docking considering protein structure variations
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Placement of medium-sized molecular fragments into active sites of proteins
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Binding site characteristics in structure-based virtual screening: evaluation of current docking tools
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A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling
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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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VMD: Visual molecular dynamics
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Recapitulation and Design of Protein Binding Peptide Structures and Sequences
inferredcites →https://doi.org/10.1016/j.jsbmb.2006.12.059openalex-snapshot
Steps towards flexible docking: Modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators’ sequences
inferredcites →https://doi.org/10.1016/j.sbi.2008.01.004openalex-snapshot
Flexible ligand docking to multiple receptor conformations: a practical alternative
inferredcites →https://doi.org/10.1021/ja0260162openalex-snapshot
Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme
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Structural Mining: Self-Consistent Design on Flexible Protein−Peptide Docking and Transferable Binding Affinity Potential
inferredcites →https://doi.org/10.1021/ja054195sopenalex-snapshot
A Flexible Docking Procedure for the Exploration of Peptide Binding Selectivity to Known Structures and Homology Models of PDZ Domains
inferredcites →https://doi.org/10.1021/ja9621760openalex-snapshot
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
inferredcites →https://doi.org/10.1021/jm020406hopenalex-snapshot
Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine
inferredcites →https://doi.org/10.1021/jm0302997openalex-snapshot
Evaluation of Docking Performance: Comparative Data on Docking Algorithms
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm050075jopenalex-snapshot
“In Situ Cross-Docking” To Simultaneously Address Multiple Targets
inferredcites →https://doi.org/10.1021/jm050540copenalex-snapshot
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
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Target Flexibility: An Emerging Consideration in Drug Discovery and Design
inferredcites →https://doi.org/10.1021/jp9708916openalex-snapshot
Structure Optimization Combining Soft-Core Interaction Functions, the Diffusion Equation Method, and Molecular Dynamics
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Recovery of known T-cell epitopes by computational scanning of a viral genome
inferredcites →https://doi.org/10.1023/b:jcam.0000017496.76572.6fopenalex-snapshot
Comparative study of several algorithms for flexible ligand docking
inferredcites →https://doi.org/10.1038/nrd2224openalex-snapshot
More than one reason to rethink the use of peptides in vaccine design
inferredcites →https://doi.org/10.1039/b509983hopenalex-snapshot
Parallel tempering: Theory, applications, and new perspectives
inferredcites →https://doi.org/10.1063/1.2888998openalex-snapshot
Hamiltonian replica exchange molecular dynamics using soft-core interactions
inferredcites →https://doi.org/10.1063/1.448118openalex-snapshot
Molecular dynamics with coupling to an external bath
inferredcites →https://doi.org/10.1073/pnas.0408857102openalex-snapshot
Comparative study of generalized Born models: Protein dynamics
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A Comparison of Non-Bonded Scaling Approaches for Free Energy Calculations
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A Leap-frog Algorithm for Stochastic Dynamics
inferredcites →https://doi.org/10.1093/bioinformatics/btl216openalex-snapshot
DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations
inferredcites →https://doi.org/10.1093/protein/6.7.723openalex-snapshot
Matching chemistry and shape in molecular docking
inferredcites →https://doi.org/10.1093/protein/gzi052openalex-snapshot
Refinement of protein cores and protein–peptide interfaces using a potential scaling approach
inferredcites →https://doi.org/10.1110/ps.04631204openalex-snapshot
Modeling the structure of bound peptide ligands to major histocompatibility complex
inferredcites →https://doi.org/10.1110/ps.051440705openalex-snapshot
Lessons from the design of a novel atomic potential for protein folding
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Advancements in the Anti-Diabetes Chemotherapeutics Based on Amino Acids, Peptides, and Peptidomimetics

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Rational Design of Peptides and Protein Molecules in Drug Discovery
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Naturstoffbasierte Aminoepoxybenzochinone inhibieren das Wachstum verschiedener Serovare des Gram‐negativen Krankheitserregers Salmonella durch Abschwächen der bakteriellen Stressabwehr
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Natural‐Product‐Inspired Aminoepoxybenzoquinones Kill Members of the Gram‐Negative Pathogen Salmonella by Attenuating Cellular Stress Response
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Acyldepsipeptide Probes Facilitate Specific Detection of Caseinolytic Protease P Independent of Its Oligomeric and Activity State
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Amythiamicin D and Related Thiopeptides as Inhibitors of the Bacterial Elongation Factor EF‐Tu: Modification of the Amino Acid at Carbon Atom C2 of Ring C Dramatically Influences Activity
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Parameterization of the Hamiltonian Dielectric Solvent (HADES) Reaction‐Field Method for the Solvation Free Energies of Amino Acid Side‐Chain Analogs
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Modeling loop backbone flexibility in receptor‐ligand docking simulations
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Sub-angstrom modeling of complexes between flexible peptides and globular proteins
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Can self‐inhibitory peptides be derived from the interfaces of globular protein–protein interactions?
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BiPPred: Combined sequence‐ and structure‐based prediction of peptide binding to the Hsp70 chaperone BiP
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FlexPepDock lessons from CAPRI peptide–protein rounds and suggested new criteria for assessment of model quality and utility
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DynaBiS : A hierarchical sampling algorithm to identify flexible binding sites for large ligands and peptides
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Information-Driven Modeling of Protein-Peptide Complexes
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Application of the ATTRACT Coarse-Grained Docking and Atomistic Refinement for Predicting Peptide-Protein Interactions
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Highly Flexible Protein-Peptide Docking Using CABS-Dock
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Receptor Databases and Computational Websites for Ligand Binding
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Re-ranking of Computational Protein–Peptide Docking Solutions with Amino Acid Profiles of Rigid-Body Docking Results
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PepCrawler: A Fast RRT–Like Algorithm for High–Resolution Refinement and Binding–Affinity Estimation of Peptide Inhibitors
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Prediction of Biomolecular Complexes
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Mechanisms Inspired Targeting Peptides
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Therapeutic peptides for coronary artery diseases: in silico methods and current perspectives
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MOLS 2.0: software package for peptide modeling and protein–ligand docking
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Predicting the bioactive conformations of macrocycles: a molecular dynamics-based docking procedure with DynaDock
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Improved docking of peptides and small molecules in iMOLSDOCK
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Extensive benchmark of rDock as a peptide-protein docking tool
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Global Optimization of Protein–peptide Docking by a Filling Function Method
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In silico designing of peptide inhibitors against pregnane X receptor: the novel candidates to control drug metabolism
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Bioinformatics and Chemometrics for Discovering Biologically Active Peptides From Food Proteins
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Recent advances and challenges in peptide drug development
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In silico studies of interaction of lantibiotics with virulent proteins
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Peptide and protein in vaccine delivery
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Machine learning assessment of the binding region as a tool for more efficient computational receptor-ligand docking
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Nectamazin A from Piper crocatum as a bioactive compound against oral and throat diseases: In vitro and in silico study
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Protein-Peptide Complex Prediction through Fragment Interaction Patterns
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Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction
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Exploring Protein-Peptide Recognition Pathways Using a Supervised Molecular Dynamics Approach
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Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking
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Predicting Protein–Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment
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Amber-Compatible Parametrization Procedure for Peptide-like Compounds: Application to 1,4- and 1,5-Substituted Triazole-Based Peptidomimetics
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Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides
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Comprehensive Evaluation of Fourteen Docking Programs on Protein–Peptide Complexes
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Structure-Based Design of Non-natural Macrocyclic Peptides That Inhibit Protein–Protein Interactions
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Turning the Actin Nucleating Compound Miuraenamide into Nucleation Inhibitors
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Antimicrobial Peptide Designing and Optimization Employing Large-Scale Flexibility Analysis of Protein-Peptide Fragments
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Repurposing human kinase inhibitors to create an antibiotic active against drug-resistant Staphylococcus aureus, persisters and biofilms
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Bap (Sil1) regulates the molecular chaperone BiP by coupling release of nucleotide and substrate
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Actin stabilizing compounds show specific biological effects due to their binding mode
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DockTope: a Web-based tool for automated pMHC-I modelling
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Assessing the capability of in silico mutation protocols for predicting the finite temperature conformation of amino acids
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Assessing the performance of MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein–peptide complexes
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A modular approach to the bisbenzylisoquinoline alkaloids tetrandrine and isotetrandrine
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Divide-and-link peptide docking: a fragment-based peptide docking protocol
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Cyclisation strategies for stabilising peptides with irregular conformations
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Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding
inferred← citeshttps://doi.org/10.1063/5.0117520openalex-snapshot
Complexes++: Efficient and versatile coarse-grained simulations of protein complexes and their dense solutions
inferred← citeshttps://doi.org/10.1080/07391102.2015.1131196openalex-snapshot
Molecular modelling, synthesis and biological evaluation of peptide inhibitors as anti-angiogenic agent targeting neuropilin-1 for anticancer application
inferred← citeshttps://doi.org/10.1080/08927022.2015.1025267openalex-snapshot
XPairIt Docking Protocolfor peptide docking and analysis
inferred← citeshttps://doi.org/10.1080/14760584.2020.1794832openalex-snapshot
An overview of in silico vaccine design against different pathogens and cancer
inferred← citeshttps://doi.org/10.1093/bib/bbv008openalex-snapshot
Docking small peptides remains a great challenge: an assessment using AutoDock Vina
inferred← citeshttps://doi.org/10.1093/bib/bby080openalex-snapshot
Protein–peptide docking using CABS-dock and contact information
inferred← citeshttps://doi.org/10.1093/bioadv/vbac024openalex-snapshot
Iris Antes 1969–2021
inferred← citeshttps://doi.org/10.1093/bioinformatics/btr498openalex-snapshot
PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors
inferred← citeshttps://doi.org/10.1093/bioinformatics/btx589openalex-snapshot
GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking
inferred← citeshttps://doi.org/10.1093/nar/gkr431openalex-snapshot
Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions
inferred← citeshttps://doi.org/10.1093/nar/gku404openalex-snapshot
PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces
inferred← citeshttps://doi.org/10.1093/nar/gky357openalex-snapshot
HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm
inferred← citeshttps://doi.org/10.1093/toxsci/kfw119openalex-snapshot
Editor’s Highlight: Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS): A Web-Based Tool for Addressing the Challenges of Cross-Species Extrapolation of Chemical Toxicity
inferred← citeshttps://doi.org/10.1101/2020.11.16.384784openalex-snapshot
CAMP: a Convolutional Attention-based Neural Network for Multifaceted Peptide-protein Interaction Prediction
inferred← citeshttps://doi.org/10.1101/2021.06.16.448765openalex-snapshot
YAPP-CD: Yet another protein-peptide complex database
inferred← citeshttps://doi.org/10.1109/bibm.2013.6732759openalex-snapshot
A protein-peptide docking program with modeling receptor flexible areas
inferred← citeshttps://doi.org/10.1109/bibm.2016.7822757openalex-snapshot
Geometry based general prediction model of protein-peptide binding affinities
inferred← citeshttps://doi.org/10.1109/spac.2014.6982674openalex-snapshot
A force fields-based multi-scale docking method in drug molecular design
inferred← citeshttps://doi.org/10.1111/cbdd.13607openalex-snapshot
PepVis: An integrated peptide virtual screening pipeline for ensemble and flexible docking protocols
inferred← citeshttps://doi.org/10.1111/jfd.14120openalex-snapshot
A Review of In Silico Approaches for Discovering Natural Viral Protein Inhibitors in Aquaculture Disease Control
inferred← citeshttps://doi.org/10.1117/12.2014767openalex-snapshot
Prediction of protein-peptide interactions: application of the XPairIt API to anthrax lethal factor and substrates
inferred← citeshttps://doi.org/10.1140/epjp/i2014-14132-1openalex-snapshot
Predicting protein-ligand and protein-peptide interfaces
inferred← citeshttps://doi.org/10.11606/t.60.2014.tde-31102014-103834openalex-snapshot
Caseína quinase 1 como alvo para o planejamento de fármacos em mal de Alzheimer
inferred← citeshttps://doi.org/10.1186/1472-6807-13-s1-s11openalex-snapshot
DINC: A new AutoDock-based protocol for docking large ligands
inferred← citeshttps://doi.org/10.1186/s12900-015-0036-2openalex-snapshot
Modeling of the OX1R–orexin-A complex suggests two alternative binding modes
inferred← citeshttps://doi.org/10.1186/s12900-016-0071-7openalex-snapshot
DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005485openalex-snapshot
Modeling disordered protein interactions from biophysical principles
inferred← citeshttps://doi.org/10.1371/journal.pone.0018934openalex-snapshot
Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors
inferred← citeshttps://doi.org/10.1371/journal.pone.0058769openalex-snapshot
A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking
inferred← citeshttps://doi.org/10.1371/journal.pone.0072838openalex-snapshot
Predicting Binding within Disordered Protein Regions to Structurally Characterised Peptide-Binding Domains
inferred← citeshttps://doi.org/10.1371/journal.pone.0094769openalex-snapshot
PaFlexPepDock: Parallel Ab-Initio Docking of Peptides onto Their Receptors with Full Flexibility Based on Rosetta
inferred← citeshttps://doi.org/10.1371/journal.pone.0109154openalex-snapshot
Break CDK2/Cyclin E1 Interface Allosterically with Small Peptides
inferred← citeshttps://doi.org/10.1371/journal.pone.0205057openalex-snapshot
Ca2+ binding induced sequential allosteric activation of sortase A: An example for ion-triggered conformational selection
inferred← citeshttps://doi.org/10.1371/journal.pone.0205179openalex-snapshot
Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana
inferred← citeshttps://doi.org/10.1515/hsz-2022-0177openalex-snapshot
Distinct conformational and energetic features define the specific recognition of (di)aromatic peptide motifs by PEX14
inferred← citeshttps://doi.org/10.1517/17460441.2015.1094458openalex-snapshot
Understanding the challenges of protein flexibility in drug design
inferred← citeshttps://doi.org/10.21236/ada607933openalex-snapshot
U.S. Army Research Laboratory (ARL) XPairIt Simulator for Peptide Docking and Analysis
inferred← citeshttps://doi.org/10.2147/dddt.s159767openalex-snapshot
Computer-aided design of amino acid-based therapeutics: a review
inferred← citeshttps://doi.org/10.2174/0115680266281358240206112605openalex-snapshot
A New Advanced Approach: Design and Screening of Affinity Peptide Ligands Using Computer Simulation Techniques
inferred← citeshttps://doi.org/10.2174/0929867311320150005openalex-snapshot
Computational Peptidology: A New and Promising Approach to Therapeutic Peptide Design
inferred← citeshttps://doi.org/10.2174/1389450119666181022153016openalex-snapshot
Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective
inferred← citeshttps://doi.org/10.2174/1568026621666210119112336openalex-snapshot
A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma
inferred← citeshttps://doi.org/10.3389/fmolb.2020.00066openalex-snapshot
Bioinformatics and Biosimulations as Toolbox for Peptides and Peptidomimetics Design: Where Are We?
inferred← citeshttps://doi.org/10.3389/fmolb.2021.681617openalex-snapshot
Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering
inferred← citeshttps://doi.org/10.3390/biom15040524openalex-snapshot
Molecular Modelling in Bioactive Peptide Discovery and Characterisation
inferred← citeshttps://doi.org/10.3390/cells12071078openalex-snapshot
Development of Cyclic Peptides Targeting the Epidermal Growth Factor Receptor in Mesenchymal Triple-Negative Breast Cancer Subtype
inferred← citeshttps://doi.org/10.3390/diagnostics12122981openalex-snapshot
Immunoinformatics Approach for Epitope-Based Vaccine Design: Key Steps for Breast Cancer Vaccine
inferred← citeshttps://doi.org/10.3390/genes13122333openalex-snapshot
Molecular Characterization, Purification, and Mode of Action of Enterocin KAE01 from Lactic Acid Bacteria and Its In Silico Analysis against MDR/ESBL Pseudomonas aeruginosa
inferred← citeshttps://doi.org/10.3390/ijms20102383openalex-snapshot
A Comprehensive Review on Current Advances in Peptide Drug Development and Design
inferred← citeshttps://doi.org/10.3390/mi12060691openalex-snapshot
Toward Development of a Label-Free Detection Technique for Microfluidic Fluorometric Peptide-Based Biosensor Systems
inferred← citeshttps://doi.org/10.3390/molecules24071351openalex-snapshot
In Silico Peptide Ligation: Iterative Residue Docking and Linking as a New Approach to Predict Protein-Peptide Interactions
inferred← citeshttps://doi.org/10.3390/molecules26061664openalex-snapshot
PepFun: Open Source Protocols for Peptide-Related Computational Analysis
inferred← citeshttps://doi.org/10.3390/molecules27238282openalex-snapshot
Computer- and NMR-Aided Design of Small-Molecule Inhibitors of the Hub1 Protein
inferred← citeshttps://doi.org/10.3390/ph16081170openalex-snapshot
Design of Tetra-Peptide Ligands of Antibody Fc Regions Using In Silico Combinatorial Library Screening
inferred← citeshttps://doi.org/10.3390/ph18121777openalex-snapshot
Docking in the Dark: Insights into Protein–Protein and Protein–Ligand Blind Docking
inferred← citeshttps://doi.org/10.3410/f.731988246.793538863openalex-snapshot
Faculty Opinions recommendation of Structure-Based Design of Non-natural Macrocyclic Peptides That Inhibit Protein-Protein Interactions.
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch011openalex-snapshot
Recent Advancements in Docking Methodologies
inferred← citeshttps://doi.org/10.4018/978-1-5225-0549-5.ch033openalex-snapshot
Recent Advancements in Docking Methodologies
inferred← citeshttps://doi.org/10.4155/fmc.12.99openalex-snapshot
Recent Work In The Development And Application Of Protein–Peptide Docking
inferred← citeshttps://doi.org/10.4236/ojapps.2012.24b007openalex-snapshot
Global optimization of protein-peptide docking by a filling function method
inferred← citeshttps://doi.org/10.53964/id.2024015openalex-snapshot
Covalent Flexible Peptide Docking in Drug Discovery: Current Challenges and Potential Interventions
inferred← citeshttps://doi.org/10.5772/48418openalex-snapshot
Protein-Peptide Interactions Revolutionize Drug Development
inferred← citeshttps://doi.org/10.5935/1984-6835.20120055openalex-snapshot
Virtual Screening Strategies in Drug Design
inferred← citeshttps://doi.org/10.59717/j.xinn-drugdisc.2026.100009openalex-snapshot
The evolution of computation-driven paradigms in targeted peptide drug design: From predictive modeling to generative AI and clinical translation
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.