scholarly journals Paratope Prediction using Convolutional and Recurrent Neural Networks

2017 ◽  
Author(s):  
Edgar Liberis ◽  
Petar Veličković ◽  
Pietro Sormanni ◽  
Michele Vendruscolo ◽  
Pietro Liò
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Learning Algorithm ◽  
Hypervariable Region ◽  
Hypervariable Regions ◽  
Current State ◽  
Entire Sequence ◽  
Probabilistic Machine Learning ◽  
Rigid Docking ◽  
Speed And Accuracy

AbstractAntibodies play an essential role in the immune system of vertebrates and are vital tools in research and diagnostics. While hypervariable regions of antibodies, which are responsible for binding, can be readily identified from their amino acid sequence, it remains challenging to accurately pinpoint which amino acids will be in contact with the antigen (the paratope). In this work, we present a sequence-based probabilistic machine learning algorithm for paratope prediction, named Parapred. Parapred uses a deep-learning architecture to leverage features from both local residue neighbourhoods and across the entire sequence. The method outperforms the current state-of-the-art methodology, and only requires a stretch of amino acid sequence corresponding to a hypervariable region as an input, without any information about the antigen. We further show that our predictions can be used to improve both speed and accuracy of a rigid docking algorithm. The Parapred method is freely available at https://github.com/eliberis/parapred for download.

Amino acid sequence of the first hypervariable region of 2κ and Aλ Bence Jones cryoglobulin

1976 ◽  
Vol 13 (11) ◽  
pp. 915-919 ◽  
Author(s):  
Geraldine C. Meinke ◽  
Hans L. Spiegelberg
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Hypervariable Region

scholarly journals Characterization of the HLA-DRβ1 third hypervariable region amino acid sequence according to charge and parental inheritance in systemic sclerosis

2017 ◽  
Vol 19 (1) ◽  
Author(s):  
Coline A. Gentil ◽  
Hilary S. Gammill ◽  
Christine T. Luu ◽  
Maureen D. Mayes ◽  
Dan E. Furst ◽  
...  
Keyword(s):  
Systemic Sclerosis ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Hypervariable Region ◽  
Parental Inheritance

scholarly journals Mechanisms of Variable p44 Expression by Anaplasma phagocytophilum

2003 ◽  
Vol 71 (10) ◽  
pp. 5650-5661 ◽  
Author(s):  
Quan Lin ◽  
Yasuko Rikihisa ◽  
Norio Ohashi ◽  
Ning Zhi
Keyword(s):  
Gene Expression ◽  
Amino Acid ◽  
Anaplasma Phagocytophilum ◽  
Hypervariable Region ◽  
Amino Acid Sequences ◽  
Hypervariable Regions ◽  
Tandem Genes ◽  
Flanking Regions ◽  
Passage Cell ◽  
Expression Status

ABSTRACT The human intragranulocytic bacterium Anaplasma phagocytophilum promotes variation of P44s, which are surface-exposed proteins encoded by a p44 multigene family. In the present study, the specific p44 gene expression loci in four strains of A. phagocytophilum were identified and it was determined that each consisted of four tandem genes, tr1, omp-1X, omp-1N, and p44. A putative σ70-type promoter was found upstream of tr1. The p44 genes include a central hypervariable region flanked by conserved regions. The hypervariable region sequence in the p44 expression locus was duplicated and, regardless of the expression status, conserved at another locus in both low- and high-passage cell cultures of strain NY-37. No significant differences in the hypervariable region were found when we compared p44 sequences, at the level of cDNA, within the expression locus and within other loci in the genomes of strains NY-37 and HZ. Similarly, in cDNA isolated from patients and from assorted cultures of strains NY-31, NY-36, and NY-37, hypervariable regions of 450 deduced amino acid sequences of various p44s within each strain were found to be identical, as were those of p44 sequences in the genome of strain HZ. These data suggest that variations in p44 sequences at the level of the p44 expression locus occur through unidirectional conversion of the entire (nonsegmental) p44 hypervariable region including flanking regions with a corresponding sequence copied from one of the conserved donor p44 genomic loci. The data suggest that the P44 antigenic repertoire within the hypervariable region is restricted.

scholarly journals An immunoglobulin light chain from a lupus-prone mouse induces autoantibodies in normal mice.

1990 ◽  
Vol 171 (6) ◽  
pp. 1919-1930 ◽  
Author(s):  
A Puccetti ◽  
T Koizumi ◽  
P Migliorini ◽  
J André-Schwartz ◽  
K J Barrett ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Light Chain ◽  
Hypervariable Region ◽  
Immunoglobulin Light Chain ◽  
Antigenic Region

Autoantibodies against the 70-kD U1 RNP nucleoprotein autoantigen and DNA were elicited in normal BALB/c mice with a purified Ig light chain. This light chain, derived from a lupus-prone MRL-lpr/lpr mouse, has two distinctive properties: it contains an idiotypic marker recognized by a monoclonal MRL-lpr/lpr anti-snRNP autoantibody, and the amino acid sequence of its third hypervariable region (CDR3) is homologous to a sequence in an antigenic region of the 70-kD U1 RNP polypeptide. The results demonstrate that an Ig idiotype that mimics an autoantigen can induce autoimmunization.

scholarly journals Haloperidol binding to monoclonal antibodies. Hypervariable region amino acid sequence determination.

1988 ◽  
Vol 263 (9) ◽  
pp. 4059-4063 ◽  
Author(s):  
M A Sherman ◽  
R J Deans ◽  
M B Bolger
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Hypervariable Region ◽  
Sequence Determination

scholarly journals The amino acid sequence of a carbohydrate-containing immunoglobulin-light-chain-type amyloid-fibril protein

1985 ◽  
Vol 232 (1) ◽  
pp. 183-190 ◽  
Author(s):  
T Tveteraas ◽  
K Sletten ◽  
P Westermark
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Light Chain ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Amino Acid Residues ◽  
Hypervariable Regions ◽  
Glycosylation Sites ◽  
Amyloid Fibril Protein ◽  
Chain Type

The amino acid sequence of an amyloid-fibril protein Es492 of immunoglobulin-lambda-light-chain origin (AL) was elucidated. The amyloid fibrils were obtained from the spleen of a patient who died from systemic amyloidosis. The amino acid sequence was elucidated from structural studies of peptides derived from digestion of the protein with trypsin, thermolysin, chymotrypsin and Staphylococcus aureus V8 proteinase and from cleavage of the protein with CNBr and BNPS-skatole. A heterogeneity in the length of the polypeptide was seen in the C-terminal region. The protein was by sequence homology to other lambda-chains shown to be of the V lambda II subgroup. Although an extensive homology was seen, some amino acid residues in positions 26, 31, 32, 40, 44, 93, 97, 98 and 99 have not previously been reported in these positions of V lambda II proteins. The significance of these residues in the fibril formation is unclear. The protein was found to contain carbohydrate, with glycosylation sites in two of the hypervariable regions.

Amino acid sequence of the first hypervariable region of 2κ and Aλ Bence Jones cryoglobulin

1976 ◽  
Vol 13 (11) ◽  
pp. 915-919
Author(s):  
G Meinke
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Hypervariable Region

scholarly journals Structural correlates of cross-reactive and individual idiotypic determinants on murine antibodies to alpha-(1 leads to 3) dextran.

1980 ◽  
Vol 151 (5) ◽  
pp. 1059-1070 ◽  
Author(s):  
B Clevinger ◽  
J Schilling ◽  
L Hood ◽  
J M Davie
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Binding Proteins ◽  
Hypervariable Region ◽  
Variable Regions ◽  
The Third ◽  
Sequence Identity ◽  
V Region ◽  
First Time

For the first time V-region amino acid sequence differences have been correlated with the expression of cross-reactive and individual idiotypes through an analysis of 12 dextran-binding proteins. This correlation has been possible because of the apparent sequence identity of the corresponding lambda chains. Expression of a cross-reactive idiotype was localized to two residues and/or a carbohydrate in the second hypervariable region of the heavy chain. Two individual idiotypes correlate with the two amino acids within the third hypervariable region that comprises the D segment of the dextran-binding proteins. These results demonstrate that idiotype reagents can recognize two amino acid differences within V and D segments of classical variable regions. In anti-dextran antibodies, cross-reactive idiotypes involve V-region determinants, whereas individual idiotype determinants correlate with D-segment variation.

scholarly journals The Hypervariable Region 1 Protein of Hepatitis C Virus Broadly Reactive with Sera of Patients with Chronic Hepatitis C Has a Similar Amino Acid Sequence with the Consensus Sequence

Virology ◽  
1999 ◽  
Vol 264 (1) ◽  
pp. 153-158 ◽  
Author(s):  
Kazuo Watanabe ◽  
Kentaro Yoshioka ◽  
Hiroshi Ito ◽  
Kazumasa Watanabe ◽  
Masatoshi Ishigami ◽  
...  
Keyword(s):  
Chronic Hepatitis ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Chronic Hepatitis C ◽  
Consensus Sequence ◽  
Hypervariable Region ◽  
Hypervariable Region 1 ◽  
Similar Amino Acid

scholarly journals Presence of highly conserved idiotypic determinants in a family of antibodies that constitute an intrastrain cross-reactive idiotype.

1980 ◽  
Vol 152 (3) ◽  
pp. 703-711 ◽  
Author(s):  
E Lamoyi ◽  
P Estess ◽  
J D Capra ◽  
A Nisonoff
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Binding Site ◽  
Hypervariable Regions

It has been shown that A/J anti-p-azophenylarsonate antibodies that share a major cross-reactive idiotype (CRI) comprise a family of closely related, but nonidentical, molecules. Our results demonstrate that 12 of 14 monoclonal hybridoma products that express the CRI have in common at least one highly conserved idiotypic determinant. It is proposed that this reflects conservation of a portion of the amino acid sequence, presumably in hypervariable regions. That the conserved determinant(s0 are located in the region of the hapten-binding site is indicated by the ability of haptens to inhibit idiotype-anti-idiotype interactions involving the conserved, or public determinants.

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