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In Silico and in Vitro Elucidation of BH3 Binding Specificity toward Bcl-2

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What this work says

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

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Effective energy function for proteins in solution

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Bcl-xL and Bcl-2 expression in squamous cell carcinoma of the head and neck

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Cluster expansion models for flexible‐backbone protein energetics

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Human nuclear clusterin mediates apoptosis by interacting with Bcl‐XL through C‐terminal coiled coil domain

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Mcl‐1–Bim complexes accommodate surprising point mutations via minor structural changes

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

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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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Structure‐based prediction of protein–peptide specificity in rosetta

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Elucidating the Folding Problem of Helical Peptides using Empirical Parameters. II†. Helix Macrodipole Effects and Rational Modification of the Helical Content of Natural Peptides

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A physical model for PDZ-domain/peptide interactions

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

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Predicting peptide binding to Major Histocompatibility Complex molecules

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Structural biology of the Bcl-2 family of proteins

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BH3-only proteins: Orchestrators of apoptosis

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Interaction of a putative BH3 domain of clusterin with anti-apoptotic Bcl-2 family proteins as revealed by NMR spectroscopy

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Contemporary strategies for the stabilization of peptides in the α-helical conformation

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Backbone flexibility in computational protein design

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BH3‐ligand regulates access of MCL‐1 to its E3 ligase

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Structure-based Prediction of bZIP Partnering Specificity

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Modeling Backbone Flexibility to Achieve Sequence Diversity: The Design of Novel α-Helical Ligands for Bcl-xL

inferredcites →https://doi.org/10.1016/j.jmb.2008.05.071openalex-snapshot

Structure of the BH3 Domains from the p53-Inducible BH3-Only Proteins Noxa and Puma in Complex with Mcl-1

inferredcites →https://doi.org/10.1016/j.jmb.2010.03.058openalex-snapshot

Determinants of BH3 Binding Specificity for Mcl-1 versus Bcl-xL

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Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains

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Predictive Bcl-2 Family Binding Models Rooted in Experiment or Structure

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Differential Targeting of Prosurvival Bcl-2 Proteins by Their BH3-Only Ligands Allows Complementary Apoptotic Function

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Protein binding specificity versus promiscuity

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Protein-Peptide Interactions Adopt the Same Structural Motifs as Monomeric Protein Folds

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Identification of Structural Mechanisms of HIV-1 Protease Specificity Using Computational Peptide Docking: Implications for Drug Resistance

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The Structural Basis of Peptide-Protein Binding Strategies

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Molecular Mechanism of the Interaction between MDM2 and p53

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The Structure of a Bcl-xL/Bim Fragment Complex

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Rationale for Bcl-xL/Bad peptide complex formation from structure, mutagenesis, and biophysical studies

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Identification of Core Structural Residues in the Sequentially Diverse and Structurally Homologous Bcl-2 Family of Proteins

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A Flexible Docking Procedure for the Exploration of Peptide Binding Selectivity to Known Structures and Homology Models of PDZ Domains

inferredcites →https://doi.org/10.1038/cr.2010.149openalex-snapshot

Evidence that inhibition of BAX activation by BCL-2 involves its tight and preferential interaction with the BH3 domain of BAX

inferredcites →https://doi.org/10.1038/nature03579openalex-snapshot

An inhibitor of Bcl-2 family proteins induces regression of solid tumours

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Design of protein-interaction specificity gives selective bZIP-binding peptides

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The MCL-1 BH3 Helix is an Exclusive MCL-1 Inhibitor and Apoptosis Sensitizer

inferredcites →https://doi.org/10.1038/nprot.2007.160openalex-snapshot

Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion

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Diagnosing and exploiting cancer's addiction to blocks in apoptosis

inferredcites →https://doi.org/10.1038/nrm2308openalex-snapshot

The BCL-2 protein family: opposing activities that mediate cell death

inferredcites →https://doi.org/10.1038/onc.2009.39openalex-snapshot

BH3-only proteins in apoptosis and beyond: an overview

inferredcites →https://doi.org/10.1038/onc.2009.50openalex-snapshot

BH3-only proteins and their roles in programmed cell death

inferredcites →https://doi.org/10.1038/sj.cdd.4402178openalex-snapshot

Crystal structure of ABT-737 complexed with Bcl-xL: implications for selectivity of antagonists of the Bcl-2 family

inferredcites →https://doi.org/10.1038/sj.cdd.4402292openalex-snapshot

BH3 domains define selective inhibitory interactions with BHRF-1 and KSHV BCL-2

inferredcites →https://doi.org/10.1038/sj.cr.7310028openalex-snapshot

How the Bcl-2 family of proteins interact to regulate apoptosis

inferredcites →https://doi.org/10.1039/b903202aopenalex-snapshot

Assessment of helical interfaces in protein–protein interactions

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Small molecule obatoclax (GX15-070) antagonizes MCL-1 and overcomes MCL-1-mediated resistance to apoptosis

inferredcites →https://doi.org/10.1074/jbc.m109.040725openalex-snapshot

Conformational Changes in Bcl-2 Pro-survival Proteins Determine Their Capacity to Bind Ligands

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Novel Bcl-2 Homology-3 Domain-like Sequences Identified from Screening Randomized Peptide Libraries for Inhibitors of the Pro-survival Bcl-2 Proteins

inferredcites →https://doi.org/10.1074/mcp.m800450-mcp200openalex-snapshot

Characterization of Domain-Peptide Interaction Interface

inferredcites →https://doi.org/10.1083/jcb.200708096openalex-snapshot

A novel BH3 ligand that selectively targets Mcl-1 reveals that apoptosis can proceed without Mcl-1 degradation

inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot

The Protein Data Bank

inferredcites →https://doi.org/10.1093/nar/gkp893openalex-snapshot

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

inferredcites →https://doi.org/10.1093/nar/gkq962openalex-snapshot

3did: identification and classification of domain-based interactions of known three-dimensional structure

inferredcites →https://doi.org/10.1093/nar/gkr048openalex-snapshot

Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers

inferredcites →https://doi.org/10.1093/nar/gkr431openalex-snapshot

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

inferredcites →https://doi.org/10.1110/ps.032896.107openalex-snapshot

Hydrophile scanning as a complement to alanine scanning for exploring and manipulating protein–protein recognition: Application to the Bim BH3 domain

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The Bcl-2 Protein Family: Arbiters of Cell Survival

inferredcites →https://doi.org/10.1128/jvi.01959-10openalex-snapshot

Deerpox Virus Encodes an Inhibitor of Apoptosis That Regulates Bak and Bax

inferredcites →https://doi.org/10.1158/1078-0432.ccr-08-0144openalex-snapshot

Bcl-2 Inhibitors: Targeting Mitochondrial Apoptotic Pathways in Cancer Therapy

inferredcites →https://doi.org/10.1186/1471-2105-11-357openalex-snapshot

Interaction prediction and classification of PDZ domains

inferredcites →https://doi.org/10.1186/1471-2105-6-s4-s13openalex-snapshot

A neural strategy for the inference of SH3 domain-peptide interaction specificity

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Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity

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Contextual Specificity in Peptide-Mediated Protein Interactions

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

inferredcites →https://doi.org/10.1371/journal.ppat.1001236openalex-snapshot

Structural Basis for Apoptosis Inhibition by Epstein-Barr Virus BHRF1

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Computational Prediction of Protein–Protein Interactions

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Small-Molecule Inhibitors of Bcl-2 Family Proteins as Therapeutic Agents in Cancer

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Intrinsically Disordered Proteins in Bcl-2 Regulated Apoptosis

What points at this work

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

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Molecular determinants of the binding specificity of BH3 ligands to BclXL apoptotic repressor

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Selective Affimers Recognise the BCL‐2 Family Proteins BCL‐xL and MCL‐1 through Noncanonical Structural Motifs**

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Biophysical basis of the promiscuous binding of B‐cell lymphoma protein 2 apoptotic repressor to BH3 ligands

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Flexible Backbone Methods for Predicting and Designing Peptide Specificity

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Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein–Protein Interactions

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Prediction of peptide binding to MHC using machine learning with sequence and structure-based feature sets

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Computational Design of Selective Peptides to Discriminate between Similar PDZ Domains in an Oncogenic Pathway

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Locating Herpesvirus Bcl-2 Homologs in the Specificity Landscape of Anti-Apoptotic Bcl-2 Proteins

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Signal Propagation Within the MCL-1/BIM Protein Complex

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Structure-Based Identification of HDAC8 Non-histone Substrates

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Computational Design of BH3-Mimetic Peptide Inhibitors That Can Bind Specifically to Mcl-1 or Bcl-X L : Role of Non-Hot Spot Residues

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Discovery of Highly Bioactive Peptides through Hierarchical Structural Information and Molecular Dynamics Simulations

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Mapping the BH3 Binding Interface of Bcl-xL, Bcl-2, and Mcl-1 Using Split-Luciferase Reassembly

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Designed BH3 Peptides with High Affinity and Specificity for Targeting Mcl-1 in Cells

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