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Cavities Tell More than Sequences: Exploring Functional Relationships of Proteases via Binding Pockets

https://doi.org/10.1021/ci300550a
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What this work says

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

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Functional Classification of Protein Kinase Binding Sites Using Cavbase
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Merging chemical and biological space: Structural mapping of enzyme binding pocket space
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Surface‐based protein binding pocket similarity
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Comparing partitions
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Silhouettes: A graphical aid to the interpretation and validation of cluster analysis
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Design, synthesis, and biological activity of potent and selective inhibitors of mast cell tryptase
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Factor VIIa inhibitors: Chemical optimization, preclinical pharmacokinetics, pharmacodynamics, and efficacy in an arterial baboon thrombosis model
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Design of novel, potent, and selective human β-tryptase inhibitors based on α-keto-[1,2,4]-oxadiazoles
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Structural Mechanism of Demethylation and Inactivation of Protein Phosphatase 2A
inferredcites →https://doi.org/10.1016/j.chembiol.2003.08.010openalex-snapshot
Discovery of Inhibitors that Elucidate the Role of UCH-L1 Activity in the H1299 Lung Cancer Cell Line
inferredcites →https://doi.org/10.1016/j.drudis.2010.05.015openalex-snapshot
Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery
inferredcites →https://doi.org/10.1016/j.drudis.2011.07.010openalex-snapshot
Finding a better path to drug selectivity
inferredcites →https://doi.org/10.1016/j.jmb.2006.04.024openalex-snapshot
From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase
inferredcites →https://doi.org/10.1016/j.jmb.2006.11.037openalex-snapshot
The Crystal Structures of Human Calpains 1 and 9 Imply Diverse Mechanisms of Action and Auto-inhibition
inferredcites →https://doi.org/10.1016/j.jmva.2006.11.013openalex-snapshot
Comparing clusterings—an information based distance
inferredcites →https://doi.org/10.1016/s0022-2836(02)00811-2openalex-snapshot
A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology
inferredcites →https://doi.org/10.1016/s0969-2126(00)00551-7openalex-snapshot
Structural Basis for Inhibition Promiscuity of Dual Specific Thrombin and Factor Xa Blood Coagulation Inhibitors
inferredcites →https://doi.org/10.1016/s0969-2126(99)80083-5openalex-snapshot
Crystal structure of human bleomycin hydrolase, a self-compartmentalizing cysteine protease
inferredcites →https://doi.org/10.1016/s1093-3263(98)00002-3openalex-snapshot
LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
inferredcites →https://doi.org/10.1021/bi971403nopenalex-snapshot
Crystal Structure of Phenylmethanesulfonyl Fluoride-Treated Human Chymase at 1.9 Å
inferredcites →https://doi.org/10.1021/ci0600509openalex-snapshot
SHED: Shannon Entropy Descriptors from Topological Feature Distributions
inferredcites →https://doi.org/10.1021/ci1001263openalex-snapshot
Predicting Polypharmacology by Binding Site Similarity: From Kinases to the Protein Universe
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Pocket Similarity: Are α Carbons Enough?
inferredcites →https://doi.org/10.1021/ci800289yopenalex-snapshot
Binding Site Similarity Analysis for the Functional Classification of the Protein Kinase Family
inferredcites →https://doi.org/10.1021/jm00049a008openalex-snapshot
Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors
inferredcites →https://doi.org/10.1021/jm030912mopenalex-snapshot
Unexpected Nanomolar Inhibition of Carbonic Anhydrase by COX-2-Selective Celecoxib: New Pharmacological Opportunities Due to Related Binding Site Recognition
inferredcites →https://doi.org/10.1021/jm2010332openalex-snapshot
Rational Approaches to Improving Selectivity in Drug Design
inferredcites →https://doi.org/10.1021/jm9804580openalex-snapshot
1,2-Benzisothiazol-3-one 1,1-Dioxide Inhibitors of Human Mast Cell Tryptase
inferredcites →https://doi.org/10.1023/a:1012801612483openalex-snapshot
On Clustering Validation Techniques
inferredcites →https://doi.org/10.1038/nbt1284openalex-snapshot
Relating protein pharmacology by ligand chemistry
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Crystal structure of human otubain 2
inferredcites →https://doi.org/10.1039/b905821bopenalex-snapshot
The topology of drug–target interaction networks: implicit dependence on drug properties and target families
inferredcites →https://doi.org/10.1073/pnas.0510403103openalex-snapshot
Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1
inferredcites →https://doi.org/10.1073/pnas.85.8.2444openalex-snapshot
Improved tools for biological sequence comparison.
inferredcites →https://doi.org/10.1074/jbc.m409068200openalex-snapshot
A Selective, Slow Binding Inhibitor of Factor VIIa Binds to a Nonstandard Active Site Conformation and Attenuates Thrombus Formation in Vivo
inferredcites →https://doi.org/10.1074/jbc.m513331200openalex-snapshot
Substrate Profiling of Cysteine Proteases Using a Combinatorial Peptide Library Identifies Functionally Unique Specificities
inferredcites →https://doi.org/10.1074/jbc.m610372200openalex-snapshot
Development of Calpain-specific Inactivators by Screening of Positional Scanning Epoxide Libraries
inferredcites →https://doi.org/10.1074/jbc.m709530200openalex-snapshot
Molecular Basis of Prodrug Activation by Human Valacyclovirase, an α-Amino Acid Ester Hydrolase
inferredcites →https://doi.org/10.1074/mcp.m400159-mcp200openalex-snapshot
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes
inferredcites →https://doi.org/10.1093/nar/28.1.304openalex-snapshot
The ENZYME database in 2000
inferredcites →https://doi.org/10.1093/nar/gkp971openalex-snapshot
MEROPS: the peptidase database
inferredcites →https://doi.org/10.1093/nar/gkq400openalex-snapshot
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison
inferredcites →https://doi.org/10.1093/protein/12.2.85openalex-snapshot
Twilight zone of protein sequence alignments
inferredcites →https://doi.org/10.1164/ajrccm.154.3.8810600openalex-snapshot
Inhaled Tryptase Causes Bronchoconstriction in Sheep via Histamine Release
inferredcites →https://doi.org/10.1371/journal.pone.0012214openalex-snapshot
Binding of Protein Kinase Inhibitors to Synapsin I Inferred from Pair-Wise Binding Site Similarity Measurements
inferredcites →https://doi.org/10.1385/mb:31:1:055openalex-snapshot
Data Clustering in Life Sciences
inferredcites →https://doi.org/10.1517/13543776.2011.568480openalex-snapshot
Calpain inhibitors: a survey of compounds reported in the patent and scientific literature

What points at this work

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

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Privilegierte Strukturen neu betrachtet
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Privileged Structures Revisited
inferred← citeshttps://doi.org/10.1002/jmr.2727openalex-snapshot
Electrostatic recognition in substrate binding to serine proteases
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Acceleration of Binding Site Comparisons by Graph Partitioning
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A fast protein binding site comparison algorithm for proteome‐wide protein function prediction and drug repurposing
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Chemogenomics and bioinformatics approaches for prioritizing kinases as drug targets for neglected tropical diseases
inferred← citeshttps://doi.org/10.1021/ci4005783openalex-snapshot
Substrate Sequences Tell Similar Stories as Binding Cavities: Commentary
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Benchmark Data Sets for Structure-Based Computational Target Prediction
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Large-Scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real
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Data-Driven Construction of Antitumor Agents with Controlled Polypharmacology
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Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects
inferred← citeshttps://doi.org/10.1109/tcbb.2014.2325020openalex-snapshot
Extended Graph-Based Models for Enhanced Similarity Search in Cavbase
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Clustering Visual Field Test Points Based on Rates of Progression to Improve the Prediction of Future Damage
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A new method for rapid comparison of protein binding pockets by capturing spatial distributions
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Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis
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Novel pharmacological maps of protein lysine methyltransferases: key for target deorphanization
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Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos
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Mapping Glaucoma Patients' 30-2 and 10-2 Visual Fields Reveals Clusters of Test Points Damaged in the 10-2 Grid That Are Not Sampled in the Sparse 30-2 Grid
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Applications of proteochemometrics (PCM) : from species extrapolation to cell-line sensitivity modelling
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