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Rapid search for tertiary fragments reveals protein sequence–structure relationships
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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A Yellow Fluorescent Protein with Reduced Chloride Sensitivity Engineered by Loop‐Insertion
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π‐Turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence
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Assessment of template‐based protein structure predictions in CASP10
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Basic Local Alignment Search Tool
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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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Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions
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Mining Tertiary Structural Motifs for Assessment of Designability
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How do insertions affect green fluorescent protein?
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Probing Designability via a Generalized Model of Helical Bundle Geometry
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A Structural Portrait of the PDZ Domain Family
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A Structural Viral Mimic of Prosurvival Bcl-2: A Pivotal Role for Sequestering Proapoptotic Bax and Bak
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Advances and pitfalls of protein structural alignment
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Protein sequence comparison and fold recognition: progress and good-practice benchmarking
inferredcites →https://doi.org/10.1016/j.sbi.2011.05.002openalex-snapshot
Protein design with fragment databases
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Template-based structure modeling of protein–protein interactions
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Protein-Peptide Complex Prediction through Fragment Interaction Patterns
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Principles for designing ideal protein structures
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Proof of principle for epitope-focused vaccine design
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The BCL-2 protein family: opposing activities that mediate cell death
inferredcites →https://doi.org/10.1073/pnas.0605878103openalex-snapshot
Helix-packing motifs in membrane proteins
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FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately
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Searching Protein 3-D Structures in Linear Time
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Ballast : A Ball-based Algorithm for Structural Motifs
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Protein structure alignment considering phenotypic plasticity
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Integrated search and alignment of protein structures
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Rigid substructure search
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SCOP database in 2002: refinements accommodate structural genomics
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Protein structure database search and evolutionary classification
inferredcites →https://doi.org/10.1093/protein/11.9.739openalex-snapshot
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
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A revised proof of the metric properties of optimally superimposed vector sets
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Rapid calculation of RMSDs using a quaternion-based characteristic polynomial
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A solution for the best rotation to relate two sets of vectors
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Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point
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A “loop entropy reduction” phage‐display selection for folded amino acid sequences
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Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces
inferredcites →https://doi.org/10.1126/science.1202617openalex-snapshot
Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin
inferredcites →https://doi.org/10.1126/science.1209368openalex-snapshot
Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold
inferredcites →https://doi.org/10.1126/science.273.5275.595openalex-snapshot
Mapping the Protein Universe
inferredcites →https://doi.org/10.1186/1471-2105-11-25openalex-snapshot
Calibur: a tool for clustering large numbers of protein decoys
inferredcites →https://doi.org/10.1186/1471-2105-11-555openalex-snapshot
The LabelHash algorithm for substructure matching
inferredcites →https://doi.org/10.1186/1478-811x-8-8openalex-snapshot
PDZ domains and their binding partners: structure, specificity, and modification
inferredcites →https://doi.org/10.1371/journal.pcbi.1000750openalex-snapshot
Structural Characteristics of Novel Protein Folds
inferredcites →https://doi.org/10.1371/journal.pcbi.1003750openalex-snapshot
A Real-Time All-Atom Structural Search Engine for Proteins
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RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design
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A Probabilistic Fragment-Based Protein Structure Prediction Algorithm
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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inferred← citeshttps://doi.org/10.1016/j.str.2015.03.015openalex-snapshot
Tertiary Structural Propensities Reveal Fundamental Sequence/Structure Relationships
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Neuroserpin and transthyretin are extracellular chaperones that preferentially inhibit amyloid formation
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Fragment-based computational design of antibodies targeting structured epitopes
inferred← citeshttps://doi.org/10.1126/science.aav7541openalex-snapshot
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A defined structural unit enables de novo design of small-molecule–binding proteins
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Expanding the space of protein geometries by computational design of de novo fold families
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De novo design of drug-binding proteins with predictable binding energy and specificity
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De novo design of porphyrin-containing proteins as efficient and stereoselective catalysts
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Protein design by provable algorithms
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Rosetta FunFolDes – A general framework for the computational design of functional proteins
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Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites
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Sequence statistics of tertiary structural motifs reflect protein stability
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Current Computational Methods for Protein-peptide Complex Structure Prediction
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De novo designed bifunctional proteins for targeted protein degradation
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SurfDiff: protein surface profiling for selective or broadly reactive epitope prioritisation in binder and immunogen design
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Expanding all-α-helical protein space through rational computational design
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De novo design of small-molecule–induced conformational change
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