On the public citation graph

Peptidic modulators of protein‐protein interactions: Progress and challenges in computational design

0 signed · 218 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.

Claim with ORCID

Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.

See reference health

What this work says

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

inferredcites →https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-bopenalex-snapshot

Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199903)20:4<412::aid-jcc3>3.0.co;2-nopenalex-snapshot

Prodock: Software package for protein modeling and docking

inferredcites →https://doi.org/10.1002/(sici)1097-0134(1997)1+<215::aid-prot29>3.0.co;2-qopenalex-snapshot

Flexible protein–ligand docking by global energy optimization in internal coordinates

inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990101)34:1<29::aid-prot4>3.0.co;2-uopenalex-snapshot

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

inferredcites →https://doi.org/10.1002/anie.200801856openalex-snapshot

Mechanism of Fast Peptide Recognition by SH3 Domains

inferredcites →https://doi.org/10.1002/bip.10207openalex-snapshot

Gaussian docking functions

inferredcites →https://doi.org/10.1002/bip.20930openalex-snapshot

Peptides derived from HIV‐1 Rev inhibit HIV‐1 integrase in a shiftide mechanism

inferredcites →https://doi.org/10.1002/bip.21057openalex-snapshot

Structure‐activity relationship and metabolic stability studies of backbone cyclization and N‐methylation of melanocortin peptides

inferredcites →https://doi.org/10.1002/bip.360240308openalex-snapshot

Efficient monte carlo method for simulation of fluctuating conformations of native proteins

inferredcites →https://doi.org/10.1002/dmrr.881openalex-snapshot

Prevention of insulin resistance and beta‐cell loss by abrogating PKCε‐induced serine phosphorylation of muscle IRS‐1 in Psammomys obesus

inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot

CHARMM : A program for macromolecular energy, minimization, and dynamics calculations

inferredcites →https://doi.org/10.1002/med.10001openalex-snapshot

Inhibition of LFA‐1/ICAM‐1 and VLA‐4/VCAM‐1 as a therapeutic approach to inflammation and autoimmune diseases

inferredcites →https://doi.org/10.1002/prot.10608openalex-snapshot

Predicting peptide binding to MHC pockets via molecular modeling, implicit solvation, and global optimization

inferredcites →https://doi.org/10.1002/prot.20088openalex-snapshot

A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

inferredcites →https://doi.org/10.1002/prot.20149openalex-snapshot

Comparative evaluation of eight docking tools for docking and virtual screening accuracy

inferredcites →https://doi.org/10.1002/prot.20831openalex-snapshot

Ab initio prediction of peptide‐MHC binding geometry for diverse class I MHC allotypes

inferredcites →https://doi.org/10.1002/prot.21082openalex-snapshot

Protein–ligand docking: Current status and future challenges

inferredcites →https://doi.org/10.1002/prot.21296openalex-snapshot

Strategies to search and design stabilizers of protein–protein interactions: A feasibility study

inferredcites →https://doi.org/10.1002/prot.22119openalex-snapshot

Structure, dynamics, and binding thermodynamics of the v‐Src SH2 domain: Implications for drug design

inferredcites →https://doi.org/10.1006/jmbi.1994.1052openalex-snapshot

Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins

inferredcites →https://doi.org/10.1006/jmbi.1996.0477openalex-snapshot

A Fast Flexible Docking Method using an Incremental Construction Algorithm

inferredcites →https://doi.org/10.1006/jmbi.1996.0897openalex-snapshot

Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

inferredcites →https://doi.org/10.1006/jmbi.1999.3053openalex-snapshot

Miniaturized proteins: the backbone cyclic proteinomimetic approach 1 1Edited by A. R. Fersht

inferredcites →https://doi.org/10.1007/s10822-008-9216-5openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.bbrc.2008.10.166openalex-snapshot

A novel integrin α5β1 antagonistic peptide, A5-1, screened by Protein Chip system as a potent angiogenesis inhibitor

inferredcites →https://doi.org/10.1016/j.cbpa.2006.08.018openalex-snapshot

Simulations as analytical tools to understand protein aggregation and predict amyloid conformation

inferredcites →https://doi.org/10.1016/j.cbpa.2008.03.009openalex-snapshot

Peptidomimetics, a synthetic tool of drug discovery

inferredcites →https://doi.org/10.1016/j.cbpa.2008.09.023openalex-snapshot

Peptides as protein binding site mimetics

inferredcites →https://doi.org/10.1016/j.copbio.2007.05.006openalex-snapshot

Functional peptide arrays for high-throughput chemical biology based applications

inferredcites →https://doi.org/10.1016/j.copbio.2008.06.004openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.drudis.2007.06.008openalex-snapshot

A new paradigm for protein kinase inhibition: blocking phosphorylation without directly targeting ATP binding

inferredcites →https://doi.org/10.1016/j.jmb.2006.01.045openalex-snapshot

Recapitulation and Design of Protein Binding Peptide Structures and Sequences

inferredcites →https://doi.org/10.1016/j.jmb.2007.12.054openalex-snapshot

Characterization of Domain–Peptide Interaction Interface: A Case Study on the Amphiphysin-1 SH3 Domain

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.neuint.2006.07.017openalex-snapshot

Regulation of G proteins by human 5-HT1a receptor TM3/i2 and TM5/i3 loop peptides

inferredcites →https://doi.org/10.1016/j.peptides.2007.01.006openalex-snapshot

Effects of peptides derived from BACE1 catalytic domain on APP processing

inferredcites →https://doi.org/10.1016/j.phrs.2007.04.014openalex-snapshot

Insight into intra- and inter-molecular interactions of PKC: Design of specific modulators of kinase function

inferredcites →https://doi.org/10.1016/j.sbi.2006.10.008openalex-snapshot

Docking interactions in protein kinase and phosphatase networks

inferredcites →https://doi.org/10.1016/s0021-9258(17)31814-8openalex-snapshot

Agonists and antagonists of protein kinase C function, derived from its binding proteins.

inferredcites →https://doi.org/10.1016/s0169-409x(00)00129-0openalex-snapshot

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1

inferredcites →https://doi.org/10.1016/s0169-409x(96)00423-1openalex-snapshot

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

inferredcites →https://doi.org/10.1016/s0969-2126(03)00052-2openalex-snapshot

PDZ Tandem of Human Syntenin

inferredcites →https://doi.org/10.1016/s1473-3099(04)01058-8openalex-snapshot

Peptide inhibitors of virus—cell fusion: enfuvirtide as a case study in clinical discovery and development

inferredcites →https://doi.org/10.1021/ar8000603openalex-snapshot

N-Methylation of Peptides: A New Perspective in Medicinal Chemistry

inferredcites →https://doi.org/10.1021/bi061928sopenalex-snapshot

A Novel Substrate Mimetic Inhibitor of PKB/Akt Inhibits Prostate Cancer Tumor Growth in Mice by Blocking the PKB Pathway

inferredcites →https://doi.org/10.1021/bi7008135openalex-snapshot

Design, Synthesis, and Evaluation of Linear and Cyclic Peptide Ligands for PDZ10 of the Multi-PDZ Domain Protein MUPP1

inferredcites →https://doi.org/10.1021/bi800687hopenalex-snapshot

Computationally Designed Peptide Inhibitors of Protein−Protein Interactions in Membranes

inferredcites →https://doi.org/10.1021/cc700113copenalex-snapshot

Synthesis of a Novel Macrocyclic Library: Discovery of an IGF-1R Inhibitor

inferredcites →https://doi.org/10.1021/ci6003527openalex-snapshot

Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal Structures of Protein−Ligand Complexes

inferredcites →https://doi.org/10.1021/ci700086mopenalex-snapshot

Exploring Peptide-likeness of Active Molecules Using 2D Fingerprint Methods

inferredcites →https://doi.org/10.1021/ci8000474openalex-snapshot

Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO)

inferredcites →https://doi.org/10.1021/ci800174copenalex-snapshot

Approved Drug Mimics of Short Peptide Ligands from Protein Interaction Motifs

inferredcites →https://doi.org/10.1021/cr9900026openalex-snapshot

Peptide and Protein Recognition by Designed Molecules

inferredcites →https://doi.org/10.1021/ja026939xopenalex-snapshot

HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information

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/ja060830yopenalex-snapshot

Thermodynamic Basis for Promiscuity and Selectivity in Protein−Protein Interactions: PDZ Domains, a Case Study

inferredcites →https://doi.org/10.1021/ja063722kopenalex-snapshot

High-Throughput Sequence Determination of Cyclic Peptide Library Members by Partial Edman Degradation/Mass Spectrometry

inferredcites →https://doi.org/10.1021/ja804580nopenalex-snapshot

Oligo(N-aryl glycines): A New Twist on Structured Peptoids

inferredcites →https://doi.org/10.1021/jm0102598openalex-snapshot

Nanomolar Small Molecule Inhibitors for αvβ6, αvβ5, and αvβ3 Integrins

inferredcites →https://doi.org/10.1021/jm020017nopenalex-snapshot

Molecular Properties That Influence the Oral Bioavailability of Drug Candidates

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/jm701044ropenalex-snapshot

Multiple N-Methylation by a Designed Approach Enhances Receptor Selectivity

inferredcites →https://doi.org/10.1021/jm701093yopenalex-snapshot

Backbone Cyclic Peptidomimetic Melanocortin-4 Receptor Agonist as a Novel Orally Administrated Drug Lead for Treating Obesity

inferredcites →https://doi.org/10.1021/jm8006239openalex-snapshot

Exploiting Ordered Waters in Molecular Docking

inferredcites →https://doi.org/10.1021/jm800836wopenalex-snapshot

Modified Peptides as Potent Inhibitors of the Postsynaptic Density-95/N-Methyl- d -Aspartate Receptor Interaction

inferredcites →https://doi.org/10.1021/jp045424kopenalex-snapshot

Assessing the Accuracy of Metadynamics

inferredcites →https://doi.org/10.1021/jp076838ropenalex-snapshot

Stable Hairpins with β-Peptides: Route to Tackle Protein−Protein Interactions

inferredcites →https://doi.org/10.1023/a:1011115820450openalex-snapshot

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

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/nature04874openalex-snapshot

Mechanisms of drug inhibition of signalling molecules

inferredcites →https://doi.org/10.1038/nature06526openalex-snapshot

Reaching for high-hanging fruit in drug discovery at protein–protein interfaces

inferredcites →https://doi.org/10.1038/nbt.1489openalex-snapshot

Predicting PDZ domain–peptide interactions from primary sequences

inferredcites →https://doi.org/10.1038/nbt1098-919openalex-snapshot

Peptide modulators of protein–protein interactions in intracellular signaling

inferredcites →https://doi.org/10.1038/nchembio854openalex-snapshot

Bioinformatic discovery of novel bioactive peptides

inferredcites →https://doi.org/10.1038/nchembio876openalex-snapshot

Foldamers as versatile frameworks for the design and evolution of function

inferredcites →https://doi.org/10.1038/nmeth.1232openalex-snapshot

Engineering GPCR signaling pathways with RASSLs

inferredcites →https://doi.org/10.1038/nrd1384openalex-snapshot

Prospects for productivity

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/10.1038/nrd2590openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nrd892openalex-snapshot

The druggable genome

inferredcites →https://doi.org/10.1042/bj20070825openalex-snapshot

Structure-based design of small peptide inhibitors of protein kinase CK2 subunit interaction

inferredcites →https://doi.org/10.1042/bst0351021openalex-snapshot

Competitive inhibitors and allosteric activators of protein kinase C isoenzymes: a personal account and progress report on transferring academic discoveries to the clinic

inferredcites →https://doi.org/10.1073/pnas.0610494104openalex-snapshot

Ligand configurational entropy and protein binding

inferredcites →https://doi.org/10.1073/pnas.0807163105openalex-snapshot

C-terminal peptides coassemble into Aβ42 oligomers and protect neurons against Aβ42-induced neurotoxicity

inferredcites →https://doi.org/10.1074/jbc.271.24.14280openalex-snapshot

Glycan-dependent and -independent Association of Vesicular Stomatitis Virus G Protein with Calnexin

inferredcites →https://doi.org/10.1074/jbc.271.27.16384openalex-snapshot

A Peptide Derived from a β2-Adrenergic Receptor Transmembrane Domain Inhibits Both Receptor Dimerization and Activation

inferredcites →https://doi.org/10.1074/jbc.274.49.34911openalex-snapshot

Inhibition of G-protein-coupled Receptor Function by Disruption of Transmembrane Domain Interactions

inferredcites →https://doi.org/10.1074/jbc.m306723200openalex-snapshot

Sequence-based Design of Kinase Inhibitors Applicable for Therapeutics and Target Identification

inferredcites →https://doi.org/10.1074/jbc.m500577200openalex-snapshot

Molecular Determinants for the Complex Binding Specificity of the PDZ Domain in PICK1

inferredcites →https://doi.org/10.1074/jbc.r800015200openalex-snapshot

The Role of Amyloid Precursor Protein Processing by BACE1, the β-Secretase, in Alzheimer Disease Pathophysiology

inferredcites →https://doi.org/10.1098/rsif.2006.0115openalex-snapshot

Targeting protein–protein interactions by rational design: mimicry of protein surfaces

inferredcites →https://doi.org/10.1110/ps.03154503openalex-snapshot

A graph‐theory algorithm for rapid protein side‐chain prediction

inferredcites →https://doi.org/10.1110/ps.04631204openalex-snapshot

Modeling the structure of bound peptide ligands to major histocompatibility complex

inferredcites →https://doi.org/10.1111/j.1582-4934.2008.00189.xopenalex-snapshot

Phage display selection of peptides that home to atherosclerotic plaques: IL‐4 receptor as a candidate target in atherosclerosis

inferredcites →https://doi.org/10.1124/jpet.103.053843openalex-snapshot

Blockade of G Protein-Coupled Receptors and the Dopamine Transporter by a Transmembrane Domain Peptide: Novel Strategy for Functional Inhibition of Membrane Proteins in Vivo

inferredcites →https://doi.org/10.1124/mol.107.044164openalex-snapshot

Discovery of a Quorum-Sensing Inhibitor of Drug-Resistant Staphylococcal Infections by Structure-Based Virtual Screening

inferredcites →https://doi.org/10.1126/stke.3742007pe8openalex-snapshot

Meeting Report: Targeting the Kinome—20 Years of Tyrosine Kinase Inhibitor Research in BaselA report on the "Targeting the Kinome" meeting, Basel, Switzerland, 4 to 6 December 2006.

inferredcites →https://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot

Calculation of Protein-Ligand Binding Affinities

inferredcites →https://doi.org/10.1158/0008-5472.can-03-2420openalex-snapshot

LynIs a Target Gene for Prostate Cancer

inferredcites →https://doi.org/10.1182/blood-2002-12-3634openalex-snapshot

Induction of pro-angiogenic signaling by a synthetic peptide derived from the second intracellular loop of S1P3 (EDG3)

inferredcites →https://doi.org/10.1186/1471-2105-7-11openalex-snapshot

SuperMimic – Fitting peptide mimetics into protein structures

inferredcites →https://doi.org/10.1186/1471-2105-7-5openalex-snapshot

The comprehensive updated regulatory network of Escherichia coli K-12

inferredcites →https://doi.org/10.1196/annals.1378.087openalex-snapshot

Distinct Activity of Peptide Mimetic Intracellular Ligands (Pepducins) for Proteinase‐Activated Receptor‐1 in Multiple Cells/Tissues

inferredcites →https://doi.org/10.1371/journal.pbio.0060239openalex-snapshot

A Specificity Map for the PDZ Domain Family

inferredcites →https://doi.org/10.1371/journal.pcbi.1000138openalex-snapshot

Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers

inferredcites →https://doi.org/10.1371/journal.pone.0002524openalex-snapshot

Contextual Specificity in Peptide-Mediated Protein Interactions

inferredcites →https://doi.org/10.1517/17460441.3.7.761openalex-snapshot

Non-ATP-competitive kinase inhibitors – enhancing selectivity through new inhibition strategies

inferredcites →https://doi.org/10.1529/biophysj.106.097766openalex-snapshot

Role of Electrostatic Interactions in Amyloid β-Protein (Aβ) Oligomer Formation: A Discrete Molecular Dynamics Study

inferredcites →https://doi.org/10.1529/biophysj.107.106369openalex-snapshot

Insight into the Folding Inhibition of the HIV-1 Protease by a Small Peptide

inferredcites →https://doi.org/10.2144/000112045openalex-snapshot

Sequence-Based Protein Kinase Inhibition: Applications for Drug Development

inferredcites →https://doi.org/10.2174/138161207781039715openalex-snapshot

Developing Antiangiogenic Peptide Drugs for Angiogenesis-Related Diseases

inferredcites →https://doi.org/10.2174/1389557053765583openalex-snapshot

Advancements in the Anti-Diabetes Chemotherapeutics Based on Amino Acids, Peptides, and Peptidomimetics

inferredcites →https://doi.org/10.2174/156720507783018208openalex-snapshot

NAP, A Neuroprotective Drug Candidate in Clinical Trials, Stimulates Microtubule Assembly in the Living Cell

inferredcites →https://doi.org/10.2741/3175openalex-snapshot

Understanding eukaryotic linear motifs and their role in cell signaling and regulation

inferredcites →https://doi.org/10.3987/com-07-s(u)40openalex-snapshot

Synthesis of Novel Urea Bridged Macrocyclic Molecules Using BTC

What points at this work

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

inferred← citeshttps://doi.org/10.2139/ssrn.4800950openalex-extracted

PepCA: Unveiling Protein-Peptide Interaction Sites with a Multimodal Neural Network Model

inferred← citeshttps://doi.org/10.1002/9781118760369.ch7openalex-snapshot

Proteome and Peptidome Dynamics

inferred← citeshttps://doi.org/10.1002/9783527677016.ch18openalex-snapshot

Peptide Design by Nature‐Inspired Algorithms

inferred← citeshttps://doi.org/10.1002/bip.22066openalex-snapshot

Prediction of antimicrobial peptides based on the adaptive neuro‐fuzzy inference system application

inferred← citeshttps://doi.org/10.1002/chem.201501196openalex-snapshot

Metadynamics Simulations Rationalise the Conformational Effects Induced by N‐Methylation of RGD Cyclic Hexapeptides

inferred← citeshttps://doi.org/10.1002/minf.201300064openalex-snapshot

Development of QSAR‐Improved Statistical Potential for the Structure‐Based Analysis of ProteinPeptide Binding Affinities

inferred← citeshttps://doi.org/10.1002/pmic.201200051openalex-snapshot

Identification of intracellular peptides in rat adipose tissue: Insights into insulin resistance

inferred← citeshttps://doi.org/10.1002/pro.114openalex-snapshot

Rational redesign of neutral endopeptidase binding to merlin and moesin proteins

inferred← citeshttps://doi.org/10.1002/pros.21238openalex-snapshot

Inhibition of androgen receptor functions by gelsolin FxxFF peptide delivered by transfection, cell‐penetrating peptides, and lentiviral infection

inferred← citeshttps://doi.org/10.1002/prot.22716openalex-snapshot

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

inferred← citeshttps://doi.org/10.1002/prot.22785openalex-snapshot

Can self‐inhibitory peptides be derived from the interfaces of globular protein–protein interactions?

inferred← citeshttps://doi.org/10.1002/yea.1759openalex-snapshot

Target validation and ligand development for a pathogenic fungal profilin, using a knock‐down strain of pathogenic yeast Candida glabrata and structure‐based ligand design

inferred← citeshttps://doi.org/10.1007/978-1-0716-4623-6_16openalex-snapshot

Prediction of Protein–Peptide Binding Sites Using PepBCL

inferred← citeshttps://doi.org/10.1007/978-1-4939-6798-8_5openalex-snapshot

Application of the ATTRACT Coarse-Grained Docking and Atomistic Refinement for Predicting Peptide-Protein Interactions

inferred← citeshttps://doi.org/10.1007/978-1-4939-6798-8_7openalex-snapshot

AnchorDock for Blind Flexible Docking of Peptides to Proteins

inferred← citeshttps://doi.org/10.1007/978-1-4939-9446-5_12openalex-snapshot

In Silico Approaches for TRP Channel Modulation

inferred← citeshttps://doi.org/10.1007/978-1-61779-588-6_17openalex-snapshot

Modeling Peptide–Protein Interactions

inferred← citeshttps://doi.org/10.1007/978-3-030-71051-4_58openalex-snapshot

Re-ranking of Computational Protein–Peptide Docking Solutions with Amino Acid Profiles of Rigid-Body Docking Results

inferred← citeshttps://doi.org/10.1007/978-3-032-07880-3_7openalex-snapshot

Peptides and Peptidomimetics as Inhibitors of Protein–Protein Interactions

inferred← citeshttps://doi.org/10.1007/978-3-642-23038-7_7openalex-snapshot

PepCrawler: A Fast RRT–Like Algorithm for High–Resolution Refinement and Binding–Affinity Estimation of Peptide Inhibitors

inferred← citeshttps://doi.org/10.1007/978-3-642-37999-4_1openalex-snapshot

Drug Discovery by Targeting Protein–Protein Interactions

inferred← citeshttps://doi.org/10.1007/978-94-024-1069-3_8openalex-snapshot

Prediction of Biomolecular Complexes

inferred← citeshttps://doi.org/10.1007/s00214-020-02609-9openalex-snapshot

Influence of explicit water molecules on the charge migration dynamics of peptidomimetics: a DFT study

inferred← citeshttps://doi.org/10.1007/s10989-017-9627-zopenalex-snapshot

In silico designing of peptide inhibitors against pregnane X receptor: the novel candidates to control drug metabolism

inferred← citeshttps://doi.org/10.1007/s10989-019-09908-1openalex-snapshot

In Silico Designing of Peptidomimetics Enhancing Endoribonucleolytic Activities of Acinetobacter MazF Toxin as the Novel Anti-bacterial Candidates

inferred← citeshttps://doi.org/10.1016/b978-0-12-401734-4.00004-xopenalex-snapshot

Low-Abundance Protein Access by Combinatorial Peptide Libraries

inferred← citeshttps://doi.org/10.1016/j.ab.2024.115637openalex-snapshot

Protein-peptide binding residue prediction based on protein language models and cross-attention mechanism

inferred← citeshttps://doi.org/10.1016/j.bbapap.2013.01.043openalex-snapshot

Analysis of peptides secreted from cultured mouse brain tissue

inferred← citeshttps://doi.org/10.1016/j.biochi.2019.04.009openalex-snapshot

Identification of a peptide derived from a Bothrops moojeni metalloprotease with in vitro inhibitory action on the Plasmodium falciparum purine nucleoside phosphorylase enzyme (PfPNP)

inferred← citeshttps://doi.org/10.1016/j.bpc.2009.05.003openalex-snapshot

Continued development of an empirical function for predicting and rationalizing protein–protein binding affinities

inferred← citeshttps://doi.org/10.1016/j.cbpa.2013.10.011openalex-snapshot

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

inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2024.136933openalex-snapshot

GraphPBSP: Protein binding site prediction based on Graph Attention Network and pre-trained model ProstT5

inferred← citeshttps://doi.org/10.1016/j.isci.2024.110850openalex-snapshot

PepCA: Unveiling protein-peptide interaction sites with a multi-input neural network model

inferred← citeshttps://doi.org/10.1016/j.patcog.2025.112487openalex-snapshot

Language model encoded multi-scale feature fusion and transformation for predicting protein-peptide binding sites

inferred← citeshttps://doi.org/10.1016/j.sbi.2011.01.005openalex-snapshot

Three-dimensional modeling of protein interactions and complexes is going ‘omics

inferred← citeshttps://doi.org/10.1016/j.sbi.2012.05.005openalex-snapshot

Hybrid approaches to molecular simulation

inferred← citeshttps://doi.org/10.1016/j.sbi.2013.07.006openalex-snapshot

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

inferred← citeshttps://doi.org/10.1016/j.str.2015.03.010openalex-snapshot

AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking

inferred← citeshttps://doi.org/10.1016/j.str.2015.05.021openalex-snapshot

Fully Blind Peptide-Protein Docking with pepATTRACT

inferred← citeshttps://doi.org/10.1016/j.tips.2013.04.007openalex-snapshot

Targeting protein–protein interactions as an anticancer strategy

inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00058openalex-snapshot

Improving Protein–Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM–GBSA Scoring Function

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00192openalex-snapshot

Simultaneous Prediction of Interaction Sites on the Protein and Peptide Sides of Complexes through Multilayer Graph Convolutional Networks

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01471openalex-snapshot

MucLiPred: Multi-Level Contrastive Learning for Predicting Nucleic Acid Binding Residues of Proteins

inferred← citeshttps://doi.org/10.1021/acs.jctc.5b01211openalex-snapshot

An Updated Test of AMBER Force Fields and Implicit Solvent Models in Predicting the Secondary Structure of Helical, β-Hairpin, and Intrinsically Disordered Peptides

inferred← citeshttps://doi.org/10.1021/acs.jpcb.5b07050openalex-snapshot

Origin of Helical Screw Sense Selectivity Induced by Chiral Constrained Cα-Tetrasubstituted α-Amino Acids in Aib-based Peptides

inferred← citeshttps://doi.org/10.1021/acs.jpcb.6b02210openalex-snapshot

Computational Studies on Structural, Excitation, and Charge-Transfer Properties of Ureidopeptidomimetics

inferred← citeshttps://doi.org/10.1021/ci100076jopenalex-snapshot

Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation

inferred← citeshttps://doi.org/10.1021/jm2003969openalex-snapshot

Backbone Cyclic Peptide Inhibitors of Protein Kinase B (PKB/Akt)

inferred← citeshttps://doi.org/10.1021/jp510775eopenalex-snapshot

Mechanism of Stabilization of Helix Secondary Structure by Constrained Cα-Tetrasubstituted α-Amino Acids

inferred← citeshttps://doi.org/10.1021/pr2012076openalex-snapshot

Peptidomic Analysis of HEK293T Cells: Effect of the Proteasome Inhibitor Epoxomicin on Intracellular Peptides

inferred← citeshttps://doi.org/10.1038/nchem.427openalex-snapshot

Making drug design second nature

inferred← citeshttps://doi.org/10.1038/s41598-023-47624-5openalex-snapshot

PepCNN deep learning tool for predicting peptide binding residues in proteins using sequence, structural, and language model features

inferred← citeshttps://doi.org/10.1039/9781782623113-00037openalex-snapshot

Recent Advances in Macrocyclic Hsp90 Inhibitors

inferred← citeshttps://doi.org/10.1039/9781849735377-00319openalex-snapshot

Computational Strategies and Challenges for Targeting Protein–Protein Interactions with Small Molecules

inferred← citeshttps://doi.org/10.1039/b810924aopenalex-snapshot

Computational protein design, from single domain soluble proteins to membrane proteins

inferred← citeshttps://doi.org/10.1039/c003317kopenalex-snapshot

Analysis of mouse brain peptides using mass spectrometry-based peptidomics: implications for novel functions ranging from non-classical neuropeptides to microproteins

inferred← citeshttps://doi.org/10.1039/c1cc15704copenalex-snapshot

Expanding the accessible chemical space by solid phase synthesis of bicyclic homodetic peptides

inferred← citeshttps://doi.org/10.1039/c4cc08565eopenalex-snapshot

Modulating protein–protein interactions: the potential of peptides

inferred← citeshttps://doi.org/10.1039/c5ra03805gopenalex-snapshot

Model peptides containing the 3-sulfanyl-norbornene amino acid, a conformationally constrained cysteine analogue effective inducer of 3 10 -helix secondary structures

inferred← citeshttps://doi.org/10.1039/c7fd00183eopenalex-snapshot

Computational studies on ground and excited state charge transfer properties of peptidomimetics

inferred← citeshttps://doi.org/10.1074/jbc.m111.255364openalex-snapshot

Polypeptide Modulators of Caspase Recruitment Domain (CARD)-CARD-mediated Protein-Protein Interactions

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/10.1080/19336918.2016.1148865openalex-snapshot

Integrative systems and synthetic biology of cell-matrix adhesion sites

inferred← citeshttps://doi.org/10.1093/bib/bbac097openalex-snapshot

Integrated unsupervised–supervised modeling and prediction of protein–peptide affinities at structural level

inferred← citeshttps://doi.org/10.1093/bioinformatics/btac352openalex-snapshot

Predicting protein–peptide binding residues via interpretable deep learning

inferred← citeshttps://doi.org/10.1093/bioinformatics/btad718openalex-snapshot

DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model

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/btu838openalex-snapshot

Knowledge-based modeling of peptides at protein interfaces: PiPreD

inferred← citeshttps://doi.org/10.1093/bioinformatics/btx614openalex-snapshot

Structure-based prediction of protein– peptide binding regions using Random Forest

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/gkv456openalex-snapshot

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

inferred← citeshttps://doi.org/10.1093/nargab/lqaf137openalex-snapshot

An ensemble-based model comprising deep learning for predicting peptide-binding residues in proteins

inferred← citeshttps://doi.org/10.1109/csicc52343.2021.9420568openalex-snapshot

Prediction of protein–peptide-binding amino acid residues regions using machine learning algorithms

inferred← citeshttps://doi.org/10.1111/cbdd.13612openalex-snapshot

Molecular dynamics insights on the role β‐augmentation of the peptide N‐terminus with binding site β‐hairpin of proprotein convertase subtilisin/kexin 9

inferred← citeshttps://doi.org/10.1146/annurev-pharmtox-010919-023603openalex-snapshot

Proteasome Inhibitor Drugs

inferred← citeshttps://doi.org/10.11575/prism/17548openalex-snapshot

Designing Novel Peptidic Inhibitors of Beta Amyloid Oligomerization

inferred← citeshttps://doi.org/10.1186/1471-2105-15-282openalex-snapshot

Designing of peptides with desired half-life in intestine-like environment

inferred← citeshttps://doi.org/10.1186/s12859-016-1350-9openalex-snapshot

Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1002131openalex-snapshot

Binding Free Energy Landscape of Domain-Peptide Interactions

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1002288openalex-snapshot

Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1002800openalex-snapshot

Molecular Evolution of Peptide Ligands with Custom-Tailored Characteristics for Targeting of Glycostructures

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.0053263openalex-snapshot

Alterations of the Intracellular Peptidome in Response to the Proteasome Inhibitor Bortezomib

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.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.0103604openalex-snapshot

Proteasome Inhibitors Alter Levels of Intracellular Peptides in HEK293T and SH-SY5Y Cells

inferred← citeshttps://doi.org/10.1371/journal.pone.0145333openalex-snapshot

Reduced Levels of Proteasome Products in a Mouse Striatal Cell Model of Huntington’s Disease

inferred← citeshttps://doi.org/10.1371/journal.pone.0163312openalex-snapshot

Analysis of the Yeast Peptidome and Comparison with the Human Peptidome

inferred← citeshttps://doi.org/10.1530/joe-13-0625openalex-snapshot

AMPK-derived peptides reduce blood glucose levels but lead to fat retention in the liver of obese mice

inferred← citeshttps://doi.org/10.20381/ruor-6054openalex-snapshot

Investigating the Therapeutic Efficacy of a Novel Inhibitor GAP-107B8 on Ovarian Cancer Cells

inferred← citeshttps://doi.org/10.2147/aabc.s6272openalex-snapshot

Computer applications for prediction of protein–protein interactions and rational drug design

inferred← citeshttps://doi.org/10.2174/0929867311320150005openalex-snapshot

Computational Peptidology: A New and Promising Approach to Therapeutic Peptide Design

inferred← citeshttps://doi.org/10.2174/1381612811319230003openalex-snapshot

Protonation States in Molecular Dynamics Simulations of Peptide Folding and Binding

inferred← citeshttps://doi.org/10.2174/1389200219666181012151944openalex-snapshot

Machine Learning in Quantitative Protein–peptide Affinity Prediction: Implications for Therapeutic Peptide Design

inferred← citeshttps://doi.org/10.2174/1568026619666190304143354openalex-snapshot

Influence of Amino Acid Mutations and Small Molecules on Targeted Inhibition of Proteins Involved in Cancer

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/pathogens10121599openalex-snapshot

Inhibition of Viral Membrane Fusion by Peptides and Approaches to Peptide Design

inferred← citeshttps://doi.org/10.3390/pharmaceutics3040932openalex-snapshot

Ionic Channels as Targets for Drug Design: A Review on Computational Methods

inferred← citeshttps://doi.org/10.3998/ark.5550190.p008.500openalex-snapshot

Stereoselective synthesis and structure determination of a bicyclo[3.3.2]decapeptide

inferred← citeshttps://doi.org/10.4199/c00058ed1v01y201205npe003openalex-snapshot

Neuropeptides and Other Bioactive Peptides: From Discovery to Function

inferred← citeshttps://doi.org/10.70675/7dcf6f45z231cz483fzb8f5z5cd27c8b0499openalex-snapshot

Développement d'outils pour l'étude des interactions protéine-protéine

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.