FAIRsharing.htzwqf; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

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

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:28.075035

pass2
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:28.075035

Other names: pass2

PASS2 contains alignments of structural motifs of protein superfamilies. PASS2 is an automatic version of the original superfamily alignment database, CAMPASS (CAMbridge database of Protein Alignments organised as Structural Superfamilies). PASS2 contains alignments of protein structures at the superfamily level and is in direct correspondence with SCOPe 2.04 release.

Webpage:

http://caps.ncbs.res.in/pass2/

Publications: (8)

Publications
More detailed information about this field from each metasource.

JOY: protein sequence-structure representation and analysis
PMID: 9730927
metasource: Fairsharing.org
version: FAIRsharing.org: PASS2; PASS2; DOI: https://doi.org/10.25504/FAIRsharing.htzwqf; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming
PMID: 2181150
metasource: Fairsharing.org
version: FAIRsharing.org: PASS2; PASS2; DOI: https://doi.org/10.25504/FAIRsharing.htzwqf; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

PASS2: an automated database of protein alignments organised as structural superfamilies
PMID: 15059245
metasource: Fairsharing.org
version: FAIRsharing.org: PASS2; PASS2; DOI: https://doi.org/10.25504/FAIRsharing.htzwqf; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

CAMPASS: a database of structurally aligned protein superfamilies
PMID: 9753697
metasource: Fairsharing.org
version: FAIRsharing.org: PASS2; PASS2; DOI: https://doi.org/10.25504/FAIRsharing.htzwqf; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

PASS2: a semi-automated database of protein alignments organised as structural superfamilies
PMID: 11752316
metasource: Fairsharing.org
version: FAIRsharing.org: PASS2; PASS2; DOI: https://doi.org/10.25504/FAIRsharing.htzwqf; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

PASS2 version 4: an update to the database of structure-based sequence alignments of structural domain superfamilies
PMID: 22123743
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:28.075035

Protein three-dimensional structural databases: domains, structurally aligned homologues and superfamilies
PMID: 10089493
metasource: Fairsharing.org
version: FAIRsharing.org: PASS2; PASS2; DOI: https://doi.org/10.25504/FAIRsharing.htzwqf; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

http://dx.doi.org/10.1093/nar/GKR1096
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

JOY: protein sequence-structure representation and analysis PubMed citations: 145.

145 articles citing: JOY: protein sequence-structure representation and analysis

Evaluating Ylehd, a recombinant epoxide hydrolase from Yarrowia lipolytica as a potential biocatalyst for the resolution of benzyl glycidyl ether. PMID:35541265
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe. PMID:35411388
Exploring the structural basis of conformational heterogeneity and autoinhibition of human cGMP-specific protein kinase Iα through computational modelling and molecular dynamics simulations. PMID:32670503
High-throughput quantification of protein structural change reveals potential mechanisms of temperature adaptation in Mytilus mussels. PMID:32054457
Deciphering Molecular Virulence Mechanism of Mycobacterium tuberculosis Dop isopeptidase Based on Its Sequence-Structure-Function Linkage. PMID:31760575
The Molecular Organization of Human cGMP Specific Phosphodiesterase 6 (PDE6): Structural Implications of Somatic Mutations in Cancer and Retinitis Pigmentosa. PMID:30962868
PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe. PMID:30820573
Spectrum of ARSA variations in Asian Indian patients with Arylsulfatase A deficient metachromatic leukodystrophy. PMID:30674982
Computationally-driven identification of antibody epitopes. PMID:29199956
Structure-Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System. PMID:29149282
Recognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins. PMID:28526057
SDM: a server for predicting effects of mutations on protein stability. PMID:28525590
XSuLT: a web server for structural annotation and representation of sequence-structure alignments. PMID:28510698
Genomes, structural biology and drug discovery: combating the impacts of mutations in genetic disease and antibiotic resistance. PMID:28408471
Molecular Evolutionary Constraints that Determine the Avirulence State of Clostridium botulinum C2 Toxin. PMID:28382496
Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols. PMID:28188534
Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures. PMID:27964945
RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information. PMID:27717309
Gelsolin-Cu/ZnSOD interaction alters intracellular reactive oxygen species levels to promote cancer cell invasion. PMID:27391159
Examining the Conservation of Kinks in Alpha Helices. PMID:27314675
The 2.2-Angstrom resolution crystal structure of the carboxy-terminal region of ataxin-3. PMID:27047745
Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners. PMID:26615189
Novel mutations of the arylsulphatase B (ARSB) gene in Indian patients with mucopolysaccharidosis type VI. PMID:26609033
PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. PMID:26553811
PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots. PMID:26448684
CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis. PMID:25833954
Identifying and quantifying radiation damage at the atomic level. PMID:25723922
DNA repair. PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair. PMID:25574025
Conformational response to ligand binding in phosphomannomutase2: insights into inborn glycosylation disorder. PMID:25324542
Polyphony: superposition independent methods for ensemble-based drug discovery. PMID:25265915
Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type α-helical structure. PMID:24997568
Evolution of tertiary structure of viral RNA dependent polymerases. PMID:24816789
Helix kinks are equally prevalent in soluble and membrane proteins. PMID:24638929
In silico, in vitro and in vivo analysis of binding affinity between N and C-domains of Clostridium perfringens alpha toxin. PMID:24349173
Exploring fold space preferences of new-born and ancient protein superfamilies. PMID:24244135
Structural updates of alignment of protein domains and consequences on evolutionary models of domain superfamilies. PMID:24237883
LenVarDB: database of length-variant protein domains. PMID:24194591
Rebelling for a reason: protein structural "outliers". PMID:24073209
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. PMID:24059743
Elucidation of novel structural scaffold in rohu TLR2 and its binding site analysis with peptidoglycan, lipoteichoic acid and zymosan ligands, and downstream MyD88 adaptor protein. PMID:23956969
How long is a piece of loop? PMID:23638343
Predicting PDZ domain mediated protein interactions from structure. PMID:23336252
Mutual information and variants for protein domain-domain contact prediction. PMID:23244412
Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1α and PKR. PMID:23148689
Protein dynamics governed by interfaces of high polarity and low packing density. PMID:23110216
Laccase: enzyme revisited and function redefined. PMID:23100727
A structural systems biology approach for quantifying the systemic consequences of missense mutations in proteins. PMID:23093928
Integrative structural modelling of the cardiac thin filament: energetics at the interface and conservation patterns reveal a spotlight on period 2 of tropomyosin. PMID:23071391
Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins. PMID:23009691
Crystal structure of folliculin reveals a hidDENN function in genetically inherited renal cancer. PMID:22977732
Analysis of domain-swapped oligomers reveals local sequence preferences and structural imprints at the linker regions and swapped interfaces. PMID:22848353
On the utility of alternative amino acid scripts. PMID:22829727
Structural analysis and dimerization profile of the SCAN domain of the pluripotency factor Zfp206. PMID:22735705
Structural insights into the role of domain flexibility in human DNA ligase IV. PMID:22658747
Allosteric mutants show that PrfA activation is dispensable for vacuole escape but required for efficient spread and Listeria survival in vivo. PMID:22646689
Relationship between amino acid properties and functional parameters in olfactory receptors and discrimination of mutants with enhanced specificity. PMID:22594995
A unique modification of the eukaryotic initiation factor 5A shows the presence of the complete hypusine pathway in Leishmania donovani. PMID:22438895
Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes. PMID:22434880
Proline-proline-glutamic acid (PPE) protein Rv1168c of Mycobacterium tuberculosis augments transcription from HIV-1 long terminal repeat promoter. PMID:22427668
Pleiotropic roles of a ribosomal protein in Dictyostelium discoideum. PMID:22363460
HORIBALFRE program: Higher Order Residue Interactions Based ALgorithm for Fold REcognition. PMID:22355236
Characterization of spindle checkpoint kinase Mps1 reveals domain with functional and structural similarities to tetratricopeptide repeat motifs of Bub1 and BubR1 checkpoint kinases. PMID:22187426
Structural comparison of tRNA m(1)A58 methyltransferases revealed different molecular strategies to maintain their oligomeric architecture under extreme conditions. PMID:22168821
Structural analysis of prolyl oligopeptidases using molecular docking and dynamics: insights into conformational changes and ligand binding. PMID:22132071
PASS2 version 4: an update to the database of structure-based sequence alignments of structural domain superfamilies. PMID:22123743
Therapy of Fabry disease with pharmacological chaperones: from in silico predictions to in vitro tests. PMID:22004918
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. PMID:21959866
In silico approach to inhibition of signaling pathways of Toll-like receptors 2 and 4 by ST2L. PMID:21897866
A Burkholderia pseudomallei macrophage infectivity potentiator-like protein has rapamycin-inhibitable peptidylprolyl isomerase activity and pleiotropic effects on virulence. PMID:21859853
3D modeling and molecular dynamics simulation of an immune-regulatory cytokine, interleukin-10, from the Indian major carp, Catla catla. PMID:21830101
Environment specific substitution tables improve membrane protein alignment. PMID:21685065
Evolutionary reconstruction of the retromer complex and its function in Trypanosoma brucei. PMID:21502137
Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks. PMID:21445259
Structure prediction of dihydroflavonol 4- reductase and anthocyanidin synthase from spinach. PMID:21364828
Meet me halfway: when genomics meets structural bioinformatics. PMID:21350909
Structure-function relationship of cytoplasmic and nuclear IκB proteins: an in silico analysis. PMID:21203422
Diversity of beetle genes encoding novel plant cell wall degrading enzymes. PMID:21179425
MEDELLER: homology-based coordinate generation for membrane proteins. PMID:20926421
Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach. PMID:20634983
Synonymous codon usage influences the local protein structure observed. PMID:20530529
On the evolutionary conservation of hydrogen bonds made by buried polar amino acids: the hidden joists, braces and trusses of protein architecture. PMID:20513243
Developing stochastic models for spatial inference: bacterial chemotaxis. PMID:20498704
The human RPS4 paralogue on Yq11.223 encodes a structurally conserved ribosomal protein and is preferentially expressed during spermatogenesis. PMID:20459660
Identification of specific DNA binding residues in the TCP family of transcription factors in Arabidopsis. PMID:20363772
Visualization of multiple alignments, phylogenies and gene family evolution. PMID:20195253
Structural and functional restraints on the occurrence of single amino acid variations in human proteins. PMID:20169194
Structural and functional roles of coevolved sites in proteins. PMID:20066038
Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models. PMID:19756152
Structural and functional constraints in the evolution of protein families. PMID:19756040
Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions. PMID:19578383
Ensemble approach to predict specificity determinants: benchmarking and validation. PMID:19573245
Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold. PMID:19478949
Sequencing and characterization of asclepain f: the first cysteine peptidase cDNA cloned and expressed from Asclepias fruticosa latex. PMID:19455353
Ulla: a program for calculating environment-specific amino acid substitution tables. PMID:19417059
Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution. PMID:19173316
Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble. PMID:19038986
Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures. PMID:18833291
Structural analysis of FAD synthetase from Corynebacterium ammoniagenes. PMID:18811972
CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations. PMID:18513436
How reliably can we predict the reliability of protein structure predictions? PMID:18315874
IWS: integrated web server for protein sequence and structure analysis. PMID:18288329
Comparative modelling by restraint-based conformational sampling. PMID:18237407
Characterization of the Entamoeba histolytica ornithine decarboxylase-like enzyme. PMID:18235846
MegaMotifBase: a database of structural motifs in protein families and superfamilies. PMID:17933773
A dimer of the Toll-like receptor 4 cytoplasmic domain provides a specific scaffold for the recruitment of signalling adaptor proteins. PMID:17726518
PIC: Protein Interactions Calculator. PMID:17584791
Environment specific substitution tables for thermophilic proteins. PMID:17430559
Modeling the interaction of fipronil-related non-competitive antagonists with the GABA beta3-receptor. PMID:17206404
The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing. PMID:17142891
Structure of the orthorhombic form of human inosine triphosphate pyrophosphatase. PMID:17077483
Pirin regulates pyruvate catabolism by interacting with the pyruvate dehydrogenase E1 subunit and modulating pyruvate dehydrogenase activity. PMID:16980458
Disease-causing mutations in proteins: structural analysis of the CYP1B1 mutations causing primary congenital glaucoma in humans. PMID:16963504
HARMONY: a server for the assessment of protein structures. PMID:16844999
Organic anion transporting polypeptides of the OATP/SLCO superfamily: identification of new members in nonmammalian species, comparative modeling and a potential transport mode. PMID:16648940
An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements. PMID:16641487
Regulation of insulin receptor substrate 1 pleckstrin homology domain by protein kinase C: role of serine 24 phosphorylation. PMID:16574739
DMAPS: a database of multiple alignments for protein structures. PMID:16381863
Structural evolution of the protein kinase-like superfamily. PMID:16244704
DIAL: a web-based server for the automatic identification of structural domains in proteins. PMID:15980441
Unravelling the structure of the pneumococcal autolytic lysozyme. PMID:15943581
EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments. PMID:15638949
Improvement of alignment accuracy utilizing sequentially conserved motifs. PMID:15509307
Activation of a vinculin-binding site in the talin rod involves rearrangement of a five-helix bundle. PMID:15272303
CE-MC: a multiple protein structure alignment server. PMID:15215359
PASS2: an automated database of protein alignments organised as structural superfamilies. PMID:15059245
The anti-Müllerian hormone type II receptor: insights into the binding domains recognized by a monoclonal antibody and the natural ligand. PMID:14750901
HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. PMID:14681395
Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase. PMID:14633979
Comparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (betaalpha)8 phosphoenolpyruvate/pyruvate superfamily. PMID:12837791
Motif3D: Relating protein sequence motifs to 3D structure. PMID:12824320
3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs. PMID:12824319
Structural basis of regulation and substrate specificity of protein kinase CK2 deduced from the modeling of protein-protein interactions. PMID:12740046
Prediction of 5-HT3 receptor agonist-binding residues using homology modeling. PMID:12668442
Bioinformatics methods to predict protein structure and function. A practical approach. PMID:12632698
Active-site-mutagenesis study of rat liver betaine-homocysteine S-methyltransferase. PMID:12487625
Stabilizing the integrin alpha M inserted domain in alternative conformations with a range of engineered disulfide bonds. PMID:12466503
Hydrogen/deuterium exchange and mass spectrometric analysis of a protein containing multiple disulfide bonds: Solution structure of recombinant macrophage colony stimulating factor-beta (rhM-CSFbeta). PMID:12192067
Structure of the periplasmic domain of Pseudomonas aeruginosa TolA: evidence for an evolutionary relationship with the TonB transporter protein. PMID:12169623
Functional characterization and structural modelling of late gene expression factor 4 from Bombyx mori nucleopolyhedrovirus. PMID:12169097
Docking of protein models. PMID:12142443
PASS2: a semi-automated database of protein alignments organised as structural superfamilies. PMID:11752316
How common is the funnel-like energy landscape in protein-protein interactions? PMID:11468354
A method to predict residues conferring functional differences between related proteins: application to MAP kinase pathways. PMID:10794408
The TRANSPARENT TESTA GLABRA1 locus, which regulates trichome differentiation and anthocyanin biosynthesis in Arabidopsis, encodes a WD40 repeat protein. PMID:10402433
HOMSTRAD: a database of protein structure alignments for homologous families. PMID:9828015
Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming PubMed citations: 115.

115 articles citing: Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming

PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe. PMID:35411388
Functional analysis of a species-specific inhibitor selective for human Na+-coupled citrate transporter (NaCT/SLC13A5/mINDY). PMID:33079129
Superimposition of Viral Protein Structures: A Means to Decipher the Phylogenies of Viruses. PMID:33050291
Unraveling virus relationships by structure-based phylogenetic classification. PMID:32064119
Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. PMID:31681953
Understanding the impacts of missense mutations on structures and functions of human cancer-related genes: A preliminary computational analysis of the COSMIC Cancer Gene Census. PMID:31323058
PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe. PMID:30820573
An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. PMID:28777078
Accessing gap-junction channel structure-function relationships through molecular modeling and simulations. PMID:28124624
RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information. PMID:27717309
A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments. PMID:26978354
Structure-Activity Relationship of Chlorotoxin-Like Peptides. PMID:26848686
Lst4, the yeast Fnip1/2 orthologue, is a DENN-family protein. PMID:26631379
PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. PMID:26553811
The history of the CATH structural classification of protein domains. PMID:26253692
Synthetic viability genomic screening defines Sae2 function in DNA repair. PMID:25899817
CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis. PMID:25833954
Crystal structure of human soluble adenylate cyclase reveals a distinct, highly flexible allosteric bicarbonate binding pocket. PMID:24616449
A three-dimensional model of the Photosystem II reaction centre of Pisum sativum. PMID:24408780
Rebelling for a reason: protein structural "outliers". PMID:24073209
Association of putative members to family of mosquito odorant binding proteins: scoring scheme using fuzzy functional templates and cys residue positions. PMID:23908587
DoSA: Database of Structural Alignments. PMID:23846594
Comparative genomics of odorant binding proteins in Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus. PMID:23292137
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. PMID:23203986
Why does the G117H mutation considerably improve the activity of human butyrylcholinesterase against sarin? Insights from quantum mechanical/molecular mechanical free energy calculations. PMID:23092211
Crystal structure of folliculin reveals a hidDENN function in genetically inherited renal cancer. PMID:22977732
PASS2 version 4: an update to the database of structure-based sequence alignments of structural domain superfamilies. PMID:22123743
Multi-view methods for protein structure comparison using latent dirichlet allocation. PMID:21685102
Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility. PMID:21465562
Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks. PMID:21445259
Meet me halfway: when genomics meets structural bioinformatics. PMID:21350909
Implication of porins in beta-lactam resistance of Providencia stuartii. PMID:20667831
Alignment of multiple protein structures based on sequence and structure features. PMID:19587024
In silico studies on DARC. PMID:19519483
Sequencing and characterization of asclepain f: the first cysteine peptidase cDNA cloned and expressed from Asclepias fruticosa latex. PMID:19455353
Length variations amongst protein domain superfamilies and consequences on structure and function. PMID:19333395
The meaning of alignment: lessons from structural diversity. PMID:19105835
Structural assembly of two-domain proteins by rigid-body docking. PMID:18925951
CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations. PMID:18513436
CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures. PMID:18052539
Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions. PMID:18005425
Analysis on sliding helices and strands in protein structural comparisons: a case study with protein kinases. PMID:17914234
DBAli tools: mining the protein structure space. PMID:17478513
Molecular dynamics simulation of cocaine binding with human butyrylcholinesterase and its mutants. PMID:16851561
CCR5 interactions with the variable 3 loop of gp120. PMID:16721558
Organic anion transporting polypeptides of the OATP/SLCO superfamily: identification of new members in nonmammalian species, comparative modeling and a potential transport mode. PMID:16648940
Modeling evolution of hydrogen bonding and stabilization of transition states in the process of cocaine hydrolysis catalyzed by human butyrylcholinesterase. PMID:16288482
A novel approach to structural alignment using realistic structural and environmental information. PMID:16260755
Sequence variation within botulinum neurotoxin serotypes impacts antibody binding and neutralization. PMID:16113261
Homology modeling and molecular interaction field studies of alpha-glucosidases as a guide to structure-based design of novel proposed anti-HIV inhibitors. PMID:16075303
Structural analysis of inhibition mechanisms of aurintricarboxylic acid on SARS-CoV polymerase and other proteins. PMID:15979041
Comparison of class A and D G protein-coupled receptors: common features in structure and activation. PMID:15966721
Unravelling the structure of the pneumococcal autolytic lysozyme. PMID:15943581
Molecular models of NS3 protease variants of the Hepatitis C virus. PMID:15663787
Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions. PMID:15659366
A new type of scorpion Na+-channel-toxin-like polypeptide active on K+ channels. PMID:15656785
S4: structure-based sequence alignments of SCOP superfamilies. PMID:15608181
Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach. PMID:15531607
Improvement of alignment accuracy utilizing sequentially conserved motifs. PMID:15509307
Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function. PMID:15155852
PASS2: an automated database of protein alignments organised as structural superfamilies. PMID:15059245
The BAR-domain family of proteins: a case of bending and binding? PMID:14993925
The anti-Müllerian hormone type II receptor: insights into the binding domains recognized by a monoclonal antibody and the natural ligand. PMID:14750901
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures. PMID:14715091
PFIT and PFRIT: bioinformatic algorithms for detecting glycosidase function from structure and sequence. PMID:14691237
MODBASE, a database of annotated comparative protein structure models, and associated resources. PMID:14681398
HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. PMID:14681395
Multiple structural alignment by secondary structures: algorithm and applications. PMID:14573862
Influence of a mutation in the ATP-binding region of Ca2+/calmodulin-dependent protein kinase II on its interaction with peptide substrates. PMID:14558884
Molecular modeling of the ligand-binding domains of the NR3A and NR3B subunits of the NMDA receptor. PMID:12856411
Molecular basis for fungal selectivity of novel antimitotic compounds. PMID:12821479
Active-site-mutagenesis study of rat liver betaine-homocysteine S-methyltransferase. PMID:12487625
Comparative analysis of the ligand-binding sites of the metabotropic glutamate receptors mGluR1-mGluR8. PMID:12469502
Molecular modeling of the closed forms of the kainate-binding domains of kainate receptors and qualitative analysis of the structure-activity relationships for some agonists. PMID:12469499
The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds. PMID:12461172
Structure of the periplasmic domain of Pseudomonas aeruginosa TolA: evidence for an evolutionary relationship with the TonB transporter protein. PMID:12169623
PASS2: a semi-automated database of protein alignments organised as structural superfamilies. PMID:11752316
Classification of protein disulphide-bridge topologies. PMID:11394740
Three-dimensional model of the extracellular domain of the type 4a metabotropic glutamate receptor: new insights into the activation process. PMID:11152130
PALI-a database of Phylogeny and ALIgnment of homologous protein structures. PMID:11125050
Crystal structure of the anti-(carcinoembryonic antigen) single-chain Fv antibody MFE-23 and a model for antigen binding based on intermolecular contacts. PMID:10677374
CORA--topological fingerprints for protein structural families. PMID:10211816
Protein structure comparison using iterated double dynamic programming. PMID:10091668
Analysis of interactive packing of secondary structural elements in alpha/beta units in proteins. PMID:10091660
HOMSTRAD: a database of protein structure alignments for homologous families. PMID:9828015
Structural models of antibody variable fragments: a method for investigating binding mechanisms. PMID:9690174
A unified statistical framework for sequence comparison and structure comparison. PMID:9600892
Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins. PMID:9521122
Role of sialyloligosaccharide binding in Theiler's virus persistence. PMID:9371636
A vector projection method for predicting supersecondary motifs. PMID:9008295
Patterns and conformations of commonly occurring supersecondary structures (basic motifs) in protein data bank. PMID:8968959
Wavelets and molecular structure. PMID:8877699
Predicted alpha-helix/beta-sheet secondary structures for the zinc-binding motifs of human papillomavirus E7 and E6 proteins by consensus prediction averaging and spectroscopic studies of E7. PMID:8870673
The structural alignment between two proteins: is there a unique answer? PMID:8819165
Alignment of 700 globin sequences: extent of amino acid substitution and its correlation with variation in volume. PMID:8535255
Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets. PMID:8535247
Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity. PMID:8535234
Prediction of the three-dimensional structures of the biotinylated domain from yeast pyruvate carboxylase and of the lipoylated H-protein from the pea leaf glycine cleavage system: a new automated method for the prediction of protein tertiary structure. PMID:8518734
Modeling alpha-helical transmembrane domains: the calculation and use of substitution tables for lipid-facing residues. PMID:8443590
Families and the structural relatedness among globular proteins. PMID:8318894
Catching a common fold. PMID:8318893
Comparison of conformational characteristics in structurally similar protein pairs. PMID:8268794
De novo and inverse folding predictions of protein structure and dynamics. PMID:8229093
Identity of the putative serine-proteinase fold in proteins of the complement system with nine relevant crystal structures. PMID:8216203
Structure-based identification and clustering of protein families and superfamilies. PMID:8035212
A differential geometric treatment of protein structure comparison. PMID:7920269
Multiple protein structure alignment. PMID:7849601
Derivation of rules for comparative protein modeling from a database of protein structure alignments. PMID:7833817
Models of the three-dimensional structures of echidna, horse, and pigeon lysozymes: calcium-binding lysozymes and their relationship with alpha-lactalbumins. PMID:7832986
A comparison of X-ray and NMR structures for human endothelin-1. PMID:7773179
Molecular evolution and domain structure of plasminogen-related growth factors (HGF/SF and HGF1/MSP). PMID:7756992
A structural comparison of 21 inhibitor complexes of the aspartic proteinase from Endothia parasitica. PMID:7703859
Knowledge-based model building of proteins: concepts and examples. PMID:7505680
Structure-function relationships in the cysteine proteinases actinidin, papain and papaya proteinase omega. Three-dimensional structure of papaya proteinase omega deduced by knowledge-based modelling and active-centre characteristics determined by two-hydronic-state reactivity probe kinetics and kinetics of catalysis. PMID:1741760
A database of protein structure families with common folding motifs. PMID:1304898
PASS2: an automated database of protein alignments organised as structural superfamilies PubMed citations: 22.

22 articles citing: PASS2: an automated database of protein alignments organised as structural superfamilies

PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe. PMID:35411388
PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe. PMID:30820573
PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. PMID:26553811
Insight into a molecular interaction force supporting peptide backbones and its implication to protein loops and folding. PMID:25375237
Structural updates of alignment of protein domains and consequences on evolutionary models of domain superfamilies. PMID:24237883
Rebelling for a reason: protein structural "outliers". PMID:24073209
Overcoming sequence misalignments with weighted structural superposition. PMID:22733542
PASS2 version 4: an update to the database of structure-based sequence alignments of structural domain superfamilies. PMID:22123743
Structural and functional constraints in the evolution of protein families. PMID:19756040
Alignment of multiple protein structures based on sequence and structure features. PMID:19587024
Length variations amongst protein domain superfamilies and consequences on structure and function. PMID:19333395
The meaning of alignment: lessons from structural diversity. PMID:19105835
Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble. PMID:19038986
CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations. PMID:18513436
IWS: integrated web server for protein sequence and structure analysis. PMID:18288329
MegaMotifBase: a database of structural motifs in protein families and superfamilies. PMID:17933773
Accuracy of structure-based sequence alignment of automatic methods. PMID:17883866
On single and multiple models of protein families for the detection of remote sequence relationships. PMID:16448555
iMOTdb--a comprehensive collection of spatially interacting motifs in proteins. PMID:16381866
DMAPS: a database of multiple alignments for protein structures. PMID:16381863
GenDiS: Genomic Distribution of protein structural domain Superfamilies. PMID:15608190
S4: structure-based sequence alignments of SCOP superfamilies. PMID:15608181
CAMPASS: a database of structurally aligned protein superfamilies PubMed citations: 18.

18 articles citing: CAMPASS: a database of structurally aligned protein superfamilies

GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies. PMID:30943284
PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. PMID:26553811
Monitoring the immune response to vaccination with an inactivated vaccine associated to bovine neonatal pancytopenia by deep sequencing transcriptome analysis in cattle. PMID:24099437
Rebelling for a reason: protein structural "outliers". PMID:24073209
PASS2 version 4: an update to the database of structure-based sequence alignments of structural domain superfamilies. PMID:22123743
Accuracy of structure-based sequence alignment of automatic methods. PMID:17883866
Comparison of sequence-based and structure-based phylogenetic trees of homologous proteins: Inferences on protein evolution. PMID:17426382
Evolutionary conservation of protein backbone flexibility. PMID:17021932
Structural similarity to bridge sequence space: finding new families on the bridges. PMID:15840833
S4: structure-based sequence alignments of SCOP superfamilies. PMID:15608181
iMOT: an interactive package for the selection of spatially interacting motifs. PMID:15215459
CE-MC: a multiple protein structure alignment server. PMID:15215359
PASS2: an automated database of protein alignments organised as structural superfamilies. PMID:15059245
Improvement of comparative modeling by the application of conserved motifs amongst distantly related proteins as additional restraints. PMID:14691673
HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. PMID:14681395
Definition of the tempo of sequence diversity across an alignment and automatic identification of sequence motifs: Application to protein homologous families and superfamilies. PMID:12441381
PASS2: a semi-automated database of protein alignments organised as structural superfamilies. PMID:11752316
Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily. PMID:10704478
PASS2: a semi-automated database of protein alignments organised as structural superfamilies PubMed citations: 13.

13 articles citing: PASS2: a semi-automated database of protein alignments organised as structural superfamilies

PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe. PMID:35411388
PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe. PMID:30820573
PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. PMID:26553811
Structural updates of alignment of protein domains and consequences on evolutionary models of domain superfamilies. PMID:24237883
Rebelling for a reason: protein structural "outliers". PMID:24073209
PASS2 version 4: an update to the database of structure-based sequence alignments of structural domain superfamilies. PMID:22123743
Computational Biology and Bioinformatics: a tinge of Indian spice. PMID:17611616
On single and multiple models of protein families for the detection of remote sequence relationships. PMID:16448555
S4: structure-based sequence alignments of SCOP superfamilies. PMID:15608181
Improvement of alignment accuracy utilizing sequentially conserved motifs. PMID:15509307
When proteome meets genome: the alpha helix and the beta strand of proteins are eschewed by mRNA splice junctions and may define the minimal indivisible modules of protein architecture. PMID:15381847
PASS2: an automated database of protein alignments organised as structural superfamilies. PMID:15059245
Improvement of comparative modeling by the application of conserved motifs amongst distantly related proteins as additional restraints. PMID:14691673