FAIRsharing.r3pbp3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462

caps-db
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462

Other names: CAPS-DB, caps-db

CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps.

Webpage:

http://www.bioinsilico.org/CAPSDB

Publications:

Publications
More detailed information about this field from each metasource.

Helix capping
PMID: 9514257
metasource: Fairsharing.org
version: FAIRsharing.org: CAPS-DB ; CAPS-DB : a structural classification of helix-capping motifs; DOI: https://doi.org/10.25504/FAIRsharing.r3pbp3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

An automated classification of the structure of protein loops
PMID: 9102471
metasource: Fairsharing.org
version: FAIRsharing.org: CAPS-DB ; CAPS-DB : a structural classification of helix-capping motifs; DOI: https://doi.org/10.25504/FAIRsharing.r3pbp3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

CAPS-DB: a structural classification of helix-capping motifs
PMID: 22021380
metasource: Fairsharing.org
version: FAIRsharing.org: CAPS-DB ; CAPS-DB : a structural classification of helix-capping motifs; DOI: https://doi.org/10.25504/FAIRsharing.r3pbp3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462

http://dx.doi.org/10.1093/nar/GKR879
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Helix capping PubMed citations: 223.

223 articles citing: Helix capping

Conformational dynamics in the disordered region of human CPEB3 linked to memory consolidation. PMID:35658951
Residual Structure in the Denatured State of the Fast-Folding UBA(1) Domain from the Human DNA Excision Repair Protein HHR23A. PMID:35430812
Functional and Conformational Plasticity of an Animal Group 1 LEA Protein. PMID:35327618
Response to leucine in Schizosaccharomyces pombe (fission yeast). PMID:35325114
α-Helix stabilization by co-operative side chain charge-reinforced interactions to phosphoserine in a basic kinase-substrate motif. PMID:35212726
Tracking the amino acid changes of spike proteins across diverse host species of severe acute respiratory syndrome coronavirus 2. PMID:34877480
CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus. PMID:34765099
Denatured State Conformational Biases in Three-Helix Bundles Containing Divergent Sequences Localize near Turns and Helix Capping Residues. PMID:34606713
Do calmodulin binding IQ motifs have built-in capping domains? PMID:34392571
ENNAVIA is a novel method which employs neural networks for antiviral and anti-coronavirus activity prediction for therapeutic peptides. PMID:34297817
Identification and Characterization of Species-Specific Severe Acute Respiratory Syndrome Coronavirus 2 Physicochemical Properties. PMID:33856796
Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. PMID:33741589
The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove. PMID:33620121
In situ detection of protein interactions for recombinant therapeutic enzymes. PMID:33169829
Structural determinants of protocadherin-15 mechanics and function in hearing and balance perception. PMID:32963095
Structural Basis of the Activation of Heterotrimeric Gs-Protein by Isoproterenol-Bound β1-Adrenergic Receptor. PMID:32818430
HAPPENN is a novel tool for hemolytic activity prediction for therapeutic peptides which employs neural networks. PMID:32616760
Encoding the β-Arrestin Trafficking Fate of Ghrelin Receptor GHSR1a: C-Tail-Independent Molecular Determinants in GPCRs. PMID:32259059
A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures. PMID:31892539
Helix N-Cap Residues Drive the Acid Unfolding That Is Essential in the Action of the Toxin Colicin A. PMID:31686499
The Role of Post-translational Modifications on the Energy Landscape of Huntingtin N-Terminus. PMID:31632982
Gene-specific features enhance interpretation of mutational impact on acid α-glucosidase enzyme activity. PMID:31228295
Design of Nanoparticulate Group 2 Influenza Virus Hemagglutinin Stem Antigens That Activate Unmutated Ancestor B Cell Receptors of Broadly Neutralizing Antibody Lineages. PMID:30808695
Controlling the dynamics of the Nek2 leucine zipper by engineering of "kinetic" disulphide bonds. PMID:30707691
Electronic and Steric Control of n→π* Interactions: Stabilization of the α-Helix Conformation without a Hydrogen Bond. PMID:30548564
Uncoupling the Folding and Binding of an Intrinsically Disordered Protein. PMID:29890118
Order, Disorder, and Temperature-Driven Compaction in a Designed Elastin Protein. PMID:29461832
Design of a Short Thermally Stable α-Helix Embedded in a Macrocycle. PMID:29417711
Characteristics of a PHD Finger Subtype. PMID:29253329
A tyrosinase, mTyr-CNK, that is functionally available as a monophenol monooxygenase. PMID:29222480
Features of reactive cysteines discovered through computation: from kinase inhibition to enrichment around protein degrons. PMID:29180682
A new structural arrangement in proteins involving lysine NH3+ group and carbonyl. PMID:29180642
The leukotriene B4 receptor BLT1 is stabilized by transmembrane helix capping mutations. PMID:29124210
The polypeptide biophysics of proline/alanine-rich sequences (PAS): Recombinant biopolymers with PEG-like properties. PMID:29076532
The Effects of One Amino Acid Substitutions at the C-Terminal Region of Thermostable L2 Lipase by Computational and Experimental Approach. PMID:29058211
Hydrocarbon constrained peptides - understanding preorganisation and binding affinity. PMID:28970875
The Hsp70 interdomain linker is a dynamic switch that enables allosteric communication between two structured domains. PMID:28754691
Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34. PMID:28665339
Structural Basis of TPR-Mediated Oligomerization and Activation of Oncogenic Fusion Kinases. PMID:28528776
The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins. PMID:28516010
NMR solution structure of the RED subdomain of the Sleeping Beauty transposase. PMID:28345263
Stapled Voltage-Gated Calcium Channel (CaV) α-Interaction Domain (AID) Peptides Act As Selective Protein-Protein Interaction Inhibitors of CaV Function. PMID:28278376
The intrinsic disorder alphabet. III. Dual personality of serine. PMID:28232888
Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR. PMID:28077807
Intrinsic α helix propensities compact hydrodynamic radii in intrinsically disordered proteins. PMID:27936491
Experimental and Computational Analysis of Protein Stabilization by Gly-to-d-Ala Substitution: A Convolution of Native State and Unfolded State Effects. PMID:27934019
Effect of Glu12-His89 Interaction on Dynamic Structures in HIV-1 p17 Matrix Protein Elucidated by NMR. PMID:27907055
Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and upon Multisite Phosphorylation. PMID:27807972
Origin of a folded repeat protein from an intrinsically disordered ancestor. PMID:27623012
A novel secondary structure based on fused five-membered rings motif. PMID:27511362
GADIS: Algorithm for designing sequences to achieve target secondary structure profiles of intrinsically disordered proteins. PMID:27503953
Miniaturizing VEGF: Peptides mimicking the discontinuous VEGF receptor-binding site modulate the angiogenic response. PMID:27498819
Beyond basins: φ,ψ preferences of a residue depend heavily on the φ,ψ values of its neighbors. PMID:27342939
DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences. PMID:27307636
Unconventional N-H…N Hydrogen Bonds Involving Proline Backbone Nitrogen in Protein Structures. PMID:27166805
On the satisfaction of backbone-carbonyl lone pairs of electrons in protein structures. PMID:26833776
New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities. PMID:26745530
Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes. PMID:26681483
Rational design of α-helical tandem repeat proteins with closed architectures. PMID:26675735
Comprehensive study of liposome-assisted synthesis of membrane proteins using a reconstituted cell-free translation system. PMID:26667602
Helix-Capping Histidines: Diversity of N-H···N Hydrogen Bond Strength Revealed by (2h)JNN Scalar Couplings. PMID:26523621
Structural principles for computational and de novo design of 4Fe-4S metalloproteins. PMID:26449207
Control over overall shape and size in de novo designed proteins. PMID:26396255
Mapping side chain interactions at protein helix termini. PMID:26209176
Organization of the multiaminoacyl-tRNA synthetase complex and the cotranslational protein folding. PMID:26131561
Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. PMID:26119925
Protein Synthesis with Ribosomes Selected for the Incorporation of β-Amino Acids. PMID:25982410
Domain movements during CCA-addition: a new function for motif C in the catalytic core of the human tRNA nucleotidyltransferases. PMID:25849199
The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and Its Connection to the Immunogenic Membrane-proximal External Region. PMID:25787074
Direct NMR detection of bifurcated hydrogen bonding in the α-helix N-caps of ankyrin repeat proteins. PMID:25578373
Single-chain protein mimetics of the N-terminal heptad-repeat region of gp41 with potential as anti-HIV-1 drugs. PMID:25489108
The influence of flanking secondary structures on amino Acid content and typical lengths of 3/10 helices. PMID:25371821
Structure and regulatory interactions of the cytoplasmic terminal domains of serotonin transporter. PMID:25093911
Side-chain conformation at the selectivity filter shapes the permeation free-energy landscape of an ion channel. PMID:25049389
Polar profile of antiviral peptides from AVPpred Database. PMID:24993579
Studies on structure-based sequence alignment and phylogenies of beta-lactamases. PMID:24966539
Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins. PMID:24932137
Secondary structure preferences of mn (2+) binding sites in bacterial proteins. PMID:24778647
Effects of side chains in helix nucleation differ from helix propagation. PMID:24753597
A frequency-based linguistic approach to protein decoding and design: Simple concepts, diverse applications, and the SCS Package. PMID:24688703
OGlcNAcylation and phosphorylation have similar structural effects in α-helices: post-translational modifications as inducible start and stop signals in α-helices, with greater structural effects on threonine modification. PMID:24641765
OGlcNAcylation and phosphorylation have opposing structural effects in tau: phosphothreonine induces particular conformational order. PMID:24559475
Striatins contain a noncanonical coiled coil that binds protein phosphatase 2A A subunit to form a 2:2 heterotetrameric core of striatin-interacting phosphatase and kinase (STRIPAK) complex. PMID:24550388
Theoretical prediction of hydrogen-bond basicity pKBHX using quantum chemical topology descriptors. PMID:24460383
Length Dependent Helix-Coil Transition Kinetics of Nine Alanine-Based Peptides. PMID:24307864
Elementary tetrahelical protein design for diverse oxidoreductase functions. PMID:24121554
A transient α-helical molecular recognition element in the disordered N-terminus of the Sgs1 helicase is critical for chromosome stability and binding of Top3/Rmi1. PMID:24038467
Structural characterization of the regulatory domain of brain carnitine palmitoyltransferase 1. PMID:24037959
The local dinucleotide preference of APOBEC3G can be altered from 5'-CC to 5'-TC by a single amino acid substitution. PMID:23938202
Testing the diffusing boundary model for the helix-coil transition in peptides. PMID:23878243
Evolution of the genetic code by incorporation of amino acids that improved or changed protein function. PMID:23743924
Asn441 plays a key role in folding and function of the Na+/I- symporter (NIS). PMID:23650190
Exploring the accessible conformations of N-terminal acetylated α-synuclein. PMID:23499431
Computationally designed peptide inhibitors of the ubiquitin E3 ligase SCF(Fbx4). PMID:23401343
Structural arrangement of the intracellular Ca2+ binding domains of the cardiac Na+/Ca2+ exchanger (NCX1.1): effects of Ca2+ binding. PMID:23233681
Inhibition of caspase-9 by stabilized peptides targeting the dimerization interface. PMID:23203690
A single missense mutation in a coiled-coil domain of Escherichia coli ribosomal protein S2 confers a thermosensitive phenotype that can be suppressed by ribosomal protein S1. PMID:23104805
The N-terminal capping propensities of the D-helix modulate the allosteric activation of the Escherichia coli cAMP receptor protein. PMID:23035121
Conformational flexibility determines selectivity and antibacterial, antiplasmodial, and anticancer potency of cationic α-helical peptides. PMID:22869378
Design and characterization of modular scaffolds for tubulin assembly. PMID:22791712
Prediction of heme binding residues from protein sequences with integrative sequence profiles. PMID:22759579
An Integrated Bioinformatics and Computational Biology Approach Identifies New BH3-Only Protein Candidates. PMID:22754595
Local structural differences in homologous proteins: specificities in different SCOP classes. PMID:22745680
End-Capped α-Helices as Modulators of Protein Function. PMID:22712023
Reducing the dimensionality of the protein-folding search problem. PMID:22692765
N-terminal acetylation of α-synuclein induces increased transient helical propensity and decreased aggregation rates in the intrinsically disordered monomer. PMID:22573613
Phosphorylation of syndapin I F-BAR domain at two helix-capping motifs regulates membrane tubulation. PMID:22355135
Identification of helix capping and b-turn motifs from NMR chemical shifts. PMID:22314702
PP6 regulatory subunit R1 is bidentate anchor for targeting protein phosphatase-6 to DNA-dependent protein kinase. PMID:22298787
Solution NMR of a 463-residue phosphohexomutase: domain 4 mobility, substates, and phosphoryl transfer defect. PMID:22242625
(φ,ψ)₂ motifs: a purely conformation-based fine-grained enumeration of protein parts at the two-residue level. PMID:22198294
CAPS-DB: a structural classification of helix-capping motifs. PMID:22021380
Computational design of thermostabilizing D-amino acid substitutions. PMID:21978298
Discovery of dual-action membrane-anchored modulators of incretin receptors. PMID:21935440
Insights into the classification of small GTPases. PMID:21918623
Structural properties of 2/2 hemoglobins: the group III protein from Helicobacter hepaticus. PMID:21445851
Helicobacter pylori NikR protein exhibits distinct conformations when bound to different promoters. PMID:21393642
Salt bridges: geometrically specific, designable interactions. PMID:21287621
Probing the structural determinants for the function of intracellular loop 2 in structurally cognate G-protein-coupled receptors. PMID:21062002
Prion disease susceptibility is affected by beta-structure folding propensity and local side-chain interactions in PrP. PMID:21041683
A conserved helical capping hydrogen bond in PAS domains controls signaling kinetics in the superfamily prototype photoactive yellow protein. PMID:20954744
Solution structure of the heterotrimeric complex between the interaction domains of RFX5 and RFXAP from the RFX gene regulatory complex. PMID:20732328
NMR Structure of the SARS-CoV Nonstructural Protein 7 in Solution at pH 6.5. PMID:20709084
Modulation of p-cyanophenylalanine fluorescence by amino acid side chains and rational design of fluorescence probes of alpha-helix formation. PMID:20565125
YopD self-assembly and binding to LcrV facilitate type III secretion activity by Yersinia pseudotuberculosis. PMID:20525687
omega-Helices in proteins. PMID:20496104
Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins. PMID:20420672
Structural basis for the high Ca2+ affinity of the ubiquitous SERCA2b Ca2+ pump. PMID:19846779
Betaalpha-hairpin clamps brace betaalphabeta modules and can make substantive contributions to the stability of TIM barrel proteins. PMID:19787060
Yeast Sec1p functions before and after vesicle docking. PMID:19776355
Mirrors in the PDB: left-handed alpha-turns guide design with D-amino acids. PMID:19772623
End-to-end and end-to-middle interhelical interactions: new classes of interacting helix pairs in protein structures. PMID:19770500
Identification of a unique "stability control region" that controls protein stability of tropomyosin: A two-stranded alpha-helical coiled-coil. PMID:19627992
Analysis of loop boundaries using different local structure assignment methods. PMID:19606500
Folding by numbers: primary sequence statistics and their use in studying protein folding. PMID:19468326
Solution- and adsorbed-state structural ensembles predicted for the statherin-hydroxyapatite system. PMID:19383454
A reexamination of correlations of amino acids with particular secondary structures. PMID:19280326
Conformational Properties of Helical Protein Polymers with Varying Densities of Chemically Reactive Groups. PMID:19180254
ProSeg: a database of local structures of protein segments. PMID:18931918
Insights into interferon regulatory factor activation from the crystal structure of dimeric IRF5. PMID:18836453
The structure of a folding intermediate provides insight into differences in immunoglobulin amyloidogenicity. PMID:18768806
Geometric constraints for porphyrin binding in helical protein binding sites. PMID:18636480
A generative, probabilistic model of local protein structure. PMID:18579771
Structures, basins, and energies: a deconstruction of the Protein Coil Library. PMID:18434497
Nature of protein family signatures: insights from singular value analysis of position-specific scoring matrices. PMID:18398479
Trapping a folding intermediate of the alpha-helix: stabilization of the pi-helix. PMID:18335996
Evolutionary Pareto-optimization of stably folding peptides. PMID:18284690
Roles of beta-turns in protein folding: from peptide models to protein engineering. PMID:18275088
An unstable head-rod junction may promote folding into the compact off-state conformation of regulated myosins. PMID:18155233
Phosphorylation of paxillin LD4 destabilizes helix formation and inhibits binding to focal adhesion kinase. PMID:18092823
Solution structure of inhibitor-free human metalloelastase (MMP-12) indicates an internal conformational adjustment. PMID:17997411
Enthalpic and entropic stages in alpha-helical peptide unfolding, from laser T-jump/UV Raman spectroscopy. PMID:17910449
Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails. PMID:17848202
Carboxyl pK(a) values, ion pairs, hydrogen bonding, and the pH-dependence of folding the hyperthermophile proteins Sac7d and Sso7d. PMID:17692336
Physical-chemical determinants of turn conformations in globular proteins. PMID:17656584
Learning biophysically-motivated parameters for alpha helix prediction. PMID:17570862
Structural and thermodynamic characterization of a cytoplasmic dynein light chain-intermediate chain complex. PMID:17551010
Molecular basis of coiled-coil formation. PMID:17438295
Unique mutational patterns in the envelope alpha 2 amphipathic helix and acquisition of length in gp120 hypervariable domains are associated with resistance to autologous neutralization of subtype C human immunodeficiency virus type 1. PMID:17360739
Analysis of an optimal hidden Markov model for secondary structure prediction. PMID:17166267
Direct detection of transient alpha-helical states in islet amyloid polypeptide. PMID:17123962
Comparative NMR study on the impact of point mutations on protein stability of Pseudomonas mendocina lipase. PMID:16823035
Structural diversity of protein segments follows a power-law distribution. PMID:16731566
Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. PMID:16571137
Genetic algorithms as a tool for helix design--computational and experimental studies on prion protein helix 1. PMID:16544054
Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. PMID:16537629
A phylogenetic and structural analysis of truncated hemoglobins. PMID:16474979
Intrinsic backbone preferences are fully present in blocked amino acids. PMID:16423894
Secondary structure assignment that accurately reflects physical and evolutionary characteristics. PMID:16351757
Energetic characterization of short helical polyalanine peptides in water: analysis of 13C=O chemical shift data. PMID:16316242
Evolutionarily conserved structural motifs in bacterial GST (glutathione S-transferase) are involved in protein folding and stability. PMID:16248855
Targeting angiogenesis: structural characterization and biological properties of a de novo engineered VEGF mimicking peptide. PMID:16186493
Gibbs sampling and helix-cap motifs. PMID:16174845
Molecular origin of polyglutamine aggregation in neurodegenerative diseases. PMID:16158094
High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases. PMID:15930006
Conformational behavior of chemically reactive alanine-rich repetitive protein polymers. PMID:15877375
Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs. PMID:15802651
The alpha-helical propensity of the cytoplasmic domain of phospholamban: a molecular dynamics simulation of the effect of phosphorylation and mutation. PMID:15764655
Secondary structural effects on protein NMR chemical shifts. PMID:15754052
Water-solubilized, cap-stabilized, helical polyalanines: calibration standards for NMR and CD analyses. PMID:15701003
Alpha-helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy. PMID:15699340
Miniaturized heme proteins: crystal structure of Co(III)-mimochrome IV. PMID:15551102
Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. PMID:15533926
Probing the instabilities in the dynamics of helical fragments from mouse PrPC. PMID:15494440
The helical alanine controversy: an (Ala)6 insertion dramatically increases helicity. PMID:15493925
Conformational transitions and glycation of serum albumin in patients with minimal-change glomerulopathy. PMID:15481604
Mimicry by asx- and ST-turns of the four main types of beta-turn in proteins. PMID:15459339
Solution structure of the RWD domain of the mouse GCN2 protein. PMID:15273307
Use of a structural alphabet for analysis of short loops connecting repetitive structures. PMID:15140270
Factors involved in the stability of isolated beta-sheets: Turn sequence, beta-sheet twisting, and hydrophobic surface burial. PMID:15044739
Steric restrictions in protein folding: an alpha-helix cannot be followed by a contiguous beta-strand. PMID:14767081
An optimal structure-discriminative amino acid index for protein fold recognition. PMID:14695283
Helix formation and the unfolded state of a 52-residue helical protein. PMID:14691233
Revisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix. PMID:14573863
Mutations in capillary morphogenesis gene-2 result in the allelic disorders juvenile hyaline fibromatosis and infantile systemic hyalinosis. PMID:12973667
Importance of alpha-helix N-capping motif in stabilization of betabetaalpha fold. PMID:12761399
Noncharged amino acid residues at the solvent-exposed positions in the middle and at the C terminus of the alpha-helix have the same helical propensity. PMID:12761387
Preorganization of molecular binding sites in designed diiron proteins. PMID:12655072
Stably folded de novo proteins from a designed combinatorial library. PMID:12493832
Consensus-derived structural determinants of the ankyrin repeat motif. PMID:12461176
Crystal structure of a 12 ANK repeat stack from human ankyrinR. PMID:12456646
Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship. PMID:12441385
Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments. PMID:12202354
Importance of secondary structural specificity determinants in protein folding: insertion of a native beta-sheet sequence into an alpha-helical coiled-coil. PMID:12021450
Amino acid intrinsic alpha-helical propensities III: positional dependence at several positions of C terminus. PMID:11910021
Structural insight into the mechanisms of targeting and signaling of focal adhesion kinase. PMID:11909967
A test of proposed rules for helix capping: implications for protein design. PMID:11847274
Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function. PMID:11790845
Native-state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations. PMID:11604542
Hydration of the peptide backbone largely defines the thermodynamic propensity scale of residues at the C' position of the C-capping box of alpha-helices. PMID:11535835
Reverse engineering the (beta/alpha )8 barrel fold. PMID:11248037
Breaking open a protein barrel. PMID:11248013
Position effect of cross-strand side-chain interactions on beta-hairpin formation. PMID:11152125
Conformational behavior of ionic self-complementary peptides. PMID:10892803
The bacterial cell-division protein ZipA and its interaction with an FtsZ fragment revealed by X-ray crystallography. PMID:10880432
Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2. PMID:10702927
Patterned library analysis: a method for the quantitative assessment of hypotheses concerning the determinants of protein structure. PMID:10611303
The turn sequence directs beta-strand alignment in designed beta-hairpins. PMID:10595526
Stable proline box motif at the N-terminal end of alpha-helices. PMID:10493574
Mutational analysis of a higher plant antenna protein provides identification of chromophores bound into multiple sites. PMID:10468561
Structure of human factor VIIa and its implications for the triggering of blood coagulation. PMID:10430872
Positional preference of proline in alpha-helices. PMID:10422838
Seeking an ancient enzyme in Methanococcus jannaschii using ORF, a program based on predicted secondary structure comparisons. PMID:9501173
An automated classification of the structure of protein loops PubMed citations: 56.

56 articles citing: An automated classification of the structure of protein loops

Benchmarking the Accuracy of AlphaFold 2 in Loop Structure Prediction. PMID:35883541
Enumeration and comprehensive in-silico modeling of three-helix bundle structures composed of typical αα-hairpins. PMID:34579643
The hairpin extension controls solvent access to the chromophore binding pocket in a bacterial phytochrome: a UV-vis absorption spectroscopy study. PMID:34460093
Current approaches to flexible loop modeling. PMID:34409304
DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins. PMID:30209260
Using feature optimization-based support vector machine method to recognize the β-hairpin motifs in enzymes. PMID:28855832
A structural and functional study on the 2-C-methyl-d-erythritol-4-phosphate cytidyltransferase (IspD) from Bacillus subtilis. PMID:27821871
Comparative Protein Structure Modeling Using MODELLER. PMID:27322406
Cardiolipin Interactions with Proteins. PMID:26300339
LoopIng: a template-based tool for predicting the structure of protein loops. PMID:26249814
Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. PMID:26119925
Creating stable stem regions for loop elongation in Fcabs - insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations. PMID:24792385
ArchDB 2014: structural classification of loops in proteins. PMID:24265221
How long is a piece of loop? PMID:23638343
A modular perspective of protein structures: application to fragment based loop modeling. PMID:22987351
N-glycosylation of enhanced aromatic sequons to increase glycoprotein stability. PMID:22782562
The importance of slow motions for protein functional loops. PMID:22314977
(φ,ψ)₂ motifs: a purely conformation-based fine-grained enumeration of protein parts at the two-residue level. PMID:22198294
Near-native protein loop sampling using nonparametric density estimation accommodating sparcity. PMID:22028638
CAPS-DB: a structural classification of helix-capping motifs. PMID:22021380
Glycosylation of the enhanced aromatic sequon is similarly stabilizing in three distinct reverse turn contexts. PMID:21825145
A new way to see RNA. PMID:21729350
Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs. PMID:21689388
Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks. PMID:21445259
A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins. PMID:21436958
Models to Approximate the Motions of Protein Loops. PMID:21031141
Template-based protein structure modeling. PMID:20835794
The effect of end constraints on protein loop kinematics. PMID:20441762
Structural characteristics of novel protein folds. PMID:20421995
Mining protein loops using a structural alphabet and statistical exceptionality. PMID:20132552
Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB). PMID:20066127
Prediction of backbone dihedral angles and protein secondary structure using support vector machines. PMID:20025785
Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction. PMID:19913486
A self-organizing algorithm for modeling protein loops. PMID:19696883
Local descriptors of protein structure: a systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions. PMID:19025980
Comparative protein structure modeling using Modeller. PMID:18428767
Prediction of the beta-hairpins in proteins using support vector machine. PMID:18071887
Minimalist explicit solvation models for surface loops in proteins. PMID:17429495
"Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence. PMID:17426380
ArchPRED: a template based loop structure prediction server. PMID:16844985
A supersecondary structure library and search algorithm for modeling loops in protein structures. PMID:16617149
Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins. PMID:16471897
Large-scale conformational dynamics of the HIV-1 integrase core domain and its catalytic loop mutants. PMID:15731379
Structural similarity of loops in protein families: toward the understanding of protein evolution. PMID:15691378
Use of a structural alphabet for analysis of short loops connecting repetitive structures. PMID:15140270
Homology modelling and molecular dynamics simulations: comparative studies of human aquaporin-1. PMID:15071758
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. PMID:14739324
ArchDB: automated protein loop classification as a tool for structural genomics. PMID:14681390
RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. PMID:12907716
Reducing the computational complexity of protein folding via fragment folding and assembly. PMID:12761388
Solution structure of a chemosensory protein from the moth Mamestra brassicae. PMID:12217077
Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. PMID:12032300
CODA: a combined algorithm for predicting the structurally variable regions of protein models. PMID:11344328
Modeling of loops in protein structures. PMID:11045621
Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2. PMID:10702927
Helix capping. PMID:9514257
CAPS-DB: a structural classification of helix-capping motifs PubMed citations: 3.

3 articles citing: CAPS-DB: a structural classification of helix-capping motifs

CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus. PMID:34765099
Do calmodulin binding IQ motifs have built-in capping domains? PMID:34392571
Mapping side chain interactions at protein helix termini. PMID:26209176
http://dx.doi.org/10.1093/nar/GKR879

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More detailed information about this field from each metasource.

atomic coordinate
metasource: Fairsharing.org
version: FAIRsharing.org: CAPS-DB ; CAPS-DB : a structural classification of helix-capping motifs; DOI: https://doi.org/10.25504/FAIRsharing.r3pbp3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

protein structure
metasource: Fairsharing.org
version: FAIRsharing.org: CAPS-DB ; CAPS-DB : a structural classification of helix-capping motifs; DOI: https://doi.org/10.25504/FAIRsharing.r3pbp3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

sequence annotation
metasource: Fairsharing.org
version: FAIRsharing.org: CAPS-DB ; CAPS-DB : a structural classification of helix-capping motifs; DOI: https://doi.org/10.25504/FAIRsharing.r3pbp3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

structure
metasource: Fairsharing.org
version: FAIRsharing.org: CAPS-DB ; CAPS-DB : a structural classification of helix-capping motifs; DOI: https://doi.org/10.25504/FAIRsharing.r3pbp3; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein structural motifs and surfaces
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462

protein folds and structural domains
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462

small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462

proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.791462

atomic coordinate protein structure sequence annotation structure structure protein structural motifs and surfaces protein folds and structural domains small molecule proteins

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