protein on Sparks Lab /categories/protein/ Recent content in protein on Sparks Lab Hugo -- gohugo.io Thu, 24 Jun 2021 00:00:00 +0000 SPOT-Contact-Single: Improving Single-Sequence-Based Prediction of Protein Contact Map using a Transformer Language Model, Large Training Set and Ensembled Deep Learning /server/spot-contact-single/ Thu, 24 Jun 2021 00:00:00 +0000 /server/spot-contact-single/ Our resources are limited. If you wish to run several batches per day please make use of the downloadable package or contact the administrator directly. E-mail address: Target (optional): Input your protein Sequences: Maximum: 50 sequences at a time. Single Line Sequence only and “>prot_id”only (FASTA format) >6KIL_A RGSATDTAATTGTASPDEPLYVQGQTELDDVTSDNDVVLADFYADWCGPCQMLEPVVETLAEQTDAAVAKIDVDENQALASAYGVRGVPTLVLFADGEQVEEVVGLQDEDALKDLIESYTELVP Check the Job Queue Status DDIG: Detecting DIsease-causing Genetic variations /server/ddig/ Sun, 13 Sep 2020 00:00:00 +0000 /server/ddig/ DDIG currently supports prediction of protein-coding non-frameshifting (NFS) indels, frameshifting (FS) indels, nonsense (protein-truncating) and synonymous (same-sense, silent) variants in the GRCh37/hg19 assembly of the human genome. E-mail address (optional): Target (optional): Input your variants (format and examples): Check the Job Queue Status Publications: Synonymous variants: M. Livingstone, L. Folkman, Y. Yang, P. SPOT-Disorder-Single: Single Sequence Protein disorder prediction /server/spot-disorder-single/ Fri, 28 Feb 2020 00:00:00 +0000 /server/spot-disorder-single/ E-mail address (optional): Target (optional): Input your protein Sequences: FASTA format >Example: 6KIL_A RGSATDTAATTGTASPDEPLYVQGQTELDDVTSDNDVVLADFYADWCGPCQMLEPVVETLAEQTDAAVAKIDVDENQALASAYGVRGVPTLVLFADGEQVEEVVGLQDEDALKDLIESYTELVP Check the Job Queue Status ## Example output SPRINT-Gly: Predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties /server/sprint-gly/ Thu, 27 Feb 2020 00:00:00 +0000 /server/sprint-gly/ Submit E-mail address (optional): Target (optional): Input your protein sequence: Only one sequence at a time >NP_035565.1 extracellular superoxide dismutase [Cu-Zn] precursor [Mus musculus] MLAFLFYGLLLAACGSVTMSNPGESSFDLADRLDPVEKIDRLDLVEKIGDTHAKVLEIWMELGRRREVDAAEMHAICRVQPSATLPPDQPQITGLVLFRQLGPGSRLEAYFSLEGFPAEQNASNRAIHVHEFGDLSQGCDSTGPHYNPMEVPHPQHPGDFGNFVVRNGQLWRHRVGLTASLAGPHAILGRSVVVHAGEDDLGKGGNQASLQNGNAGRRLACCVVGTSSSAAWESQTKERKKRRRESECKTT Species: Human Mouse Glycosylation type: N-linked O-linked header" is required -- Check the Job Queue Status Help page ## Example output SPIDER3: Capturing non-local interactions by long short term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers, and solvent accessibility /server/spider3/ Mon, 10 Feb 2020 00:00:00 +0000 /server/spider3/ Our resources are limited. If you wish to run several batches per day please make use of the downloadable package or contact the administrator directly. E-mail address (optional): Target (optional): Input your protein Sequences: Maximum: 10 sequences at a time (FASTA format) >Example: 6KIL_A RGSATDTAATTGTASPDEPLYVQGQTELDDVTSDNDVVLADFYADWCGPCQMLEPVVETLAEQTDAAVAKIDVDENQALASAYGVRGVPTLVLFADGEQVEEVVGLQDEDALKDLIESYTELVP Check the Job Queue Status ## Example output SPOT-1D-LM:Reaching Alignment-profile-based Accuracy in Predicting Protein Secondary and Tertiary Structural Properties without Alignment /server/spot-1d-lm/ Mon, 10 Feb 2020 00:00:00 +0000 /server/spot-1d-lm/ Our resources are limited. If you wish to run several batches per day please make use of the downloadable package or contact the administrator directly. -- The model only take upto a maximum of 1022 amino acid sequence. -- Currently, the Webserver is down until further notice. Please refer to the GITHUB for the local standalone. E-mail address: Target (optional): Input your protein Sequences: Maximum: 100 sequences at a time. SPOT-1D-Single: Improving the Single-Sequence-Based Prediction of Protein Secondary Structure, Backbone Angles, Solvent Accessibility and Half-Sphere Exposures using a Large Training Set and Ensembled Deep Learning /server/spot-1d-single/ Mon, 10 Feb 2020 00:00:00 +0000 /server/spot-1d-single/ Our resources are limited. If you wish to run several batches per day please make use of the downloadable package or contact the administrator directly. E-mail address: Target (optional): Input your protein Sequences: Maximum: 100 sequences at a time. Single Line Sequence only and “>prot_id”only (FASTA format) >6KIL_A RGSATDTAATTGTASPDEPLYVQGQTELDDVTSDNDVVLADFYADWCGPCQMLEPVVETLAEQTDAAVAKIDVDENQALASAYGVRGVPTLVLFADGEQVEEVVGLQDEDALKDLIESYTELVP Check the Job Queue Status SPOT-1D: Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks /server/spot-1d/ Mon, 10 Feb 2020 00:00:00 +0000 /server/spot-1d/ Our resources are limited. If you wish to run several batches per day please make use of the downloadable package or contact the administrator directly. E-mail address (optional): Target (optional): Input your protein Sequences: Maximum: 10 sequences at a time, less than 750AA each (FASTA format) >Example: 6KIL_A RGSATDTAATTGTASPDEPLYVQGQTELDDVTSDNDVVLADFYADWCGPCQMLEPVVETLAEQTDAAVAKIDVDENQALASAYGVRGVPTLVLFADGEQVEEVVGLQDEDALKDLIESYTELVP Check the Job Queue Status SPOT-Contact: Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks /server/spot-contact/ Mon, 10 Feb 2020 00:00:00 +0000 /server/spot-contact/ Our resources are limited. If you wish to run several batches per day please make use of the downloadable package or contact the administrator directly. E-mail address (optional): Target (optional): Input your protein Sequences: Maximum: 10 sequences at a time, less than 750AA each (FASTA format) >Example: 6KIL_A RGSATDTAATTGTASPDEPLYVQGQTELDDVTSDNDVVLADFYADWCGPCQMLEPVVETLAEQTDAAVAKIDVDENQALASAYGVRGVPTLVLFADGEQVEEVVGLQDEDALKDLIESYTELVP Check the Job Queue Status EASE-MM: Prediction of mutation-induced stability changes /server/ease-mm/ Wed, 05 Feb 2020 00:00:00 +0000 /server/ease-mm/ EASE-MM supports prediction of missense mutations specified as amino acid substitutions (protein input) or as nsSNV variants (genome input) in the GRCh37/hg19 assembly of the human genome. E-mail address (optional): Target (optional): Input your sequence and mutations: SEQ: my_short_seq RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE MUT: A40G L16V G4A Check the Job Queue Status Publication: SPOT-Disorder: Protein disorder prediction v1.0 /server/spot-disorder/ Fri, 31 Jan 2020 00:00:00 +0000 /server/spot-disorder/ Our resources are limited. If you wish to run several batches per day please make use of the downloadable package or contact the administrator directly. E-mail address (optional): Target (optional): Input your protein Sequences: Maximum: 10 sequences at a time (FASTA format) >Example: 6KIL_A RGSATDTAATTGTASPDEPLYVQGQTELDDVTSDNDVVLADFYADWCGPCQMLEPVVETLAEQTDAAVAKIDVDENQALASAYGVRGVPTLVLFADGEQVEEVVGLQDEDALKDLIESYTELVP Check the Job Queue Status ## Example output SPOT-CBP: Template-based identification of carbohydrate-binding proteins /server/spot-cbp/ Thu, 23 Jan 2020 00:00:00 +0000 /server/spot-cbp/ E-mail address (optional): Target (optional): PDB File: Input structure File MUST be in PDB format ## Example output SPOT-Disorder2: Protein disorder prediction /server/spot-disorder2/ Thu, 23 Jan 2020 00:00:00 +0000 /server/spot-disorder2/ Our resources are limited. If you wish to run several batches per day please make use of the downloadable package or contact the administrator directly. E-mail address (optional): Target (optional): Input your protein Sequences: Maximum: 10 sequences at a time, less than 750AA each (FASTA format) >Example: 6KIL_A RGSATDTAATTGTASPDEPLYVQGQTELDDVTSDNDVVLADFYADWCGPCQMLEPVVETLAEQTDAAVAKIDVDENQALASAYGVRGVPTLVLFADGEQVEEVVGLQDEDALKDLIESYTELVP Check the Job Queue Status SPOT-MoRF: Molecular recognition Features in Intrinsically Disordered Regions by Transfer Learning /server/spot-morf/ Thu, 23 Jan 2020 00:00:00 +0000 /server/spot-morf/ Our resources are limited. If you wish to run several batches per day please make use of the downloadable package or contact the administrator directly. E-mail address (optional): Target (optional): Input your protein Sequences: Maximum: 10 sequences at a time, less than 750AA each (FASTA format) >Example: 6KIL_A RGSATDTAATTGTASPDEPLYVQGQTELDDVTSDNDVVLADFYADWCGPCQMLEPVVETLAEQTDAAVAKIDVDENQALASAYGVRGVPTLVLFADGEQVEEVVGLQDEDALKDLIESYTELVP Check the Job Queue Status SPOT-Ligand2: Small molecule virtual screening by binding homology on expanded template library /server/spot-ligand2/ Wed, 22 Jan 2020 00:00:00 +0000 /server/spot-ligand2/ E-mail address (optional): Target (optional): PDB File: Custom library (Optional): Input structure File MUST be in PDB format Input compound library MUST be in SMILES format - maximum 10,000 compounds ## Example output SPOT-Ligand: Small molecule virtual screening by binding homology search /server/spot-ligand/ Wed, 22 Jan 2020 00:00:00 +0000 /server/spot-ligand/ E-mail address (optional): Target (optional): PDB File: Input structure File MUST be in PDB format ## Example output SPARKS-X: Protein fold recognition /server/sparks-x/ Wed, 15 Jan 2020 00:00:00 +0000 /server/sparks-x/ E-mail address (optional): Target (optional): Input your protein Sequences: Maximum: 500 AA, Only one protein sequence at a time >Example: 6KIL_A RGSATDTAATTGTASPDEPLYVQGQTELDDVTSDNDVVLADFYADWCGPCQMLEPVVETLAEQTDAAVAKIDVDENQALASAYGVRGVPTLVLFADGEQVEEVVGLQDEDALKDLIESYTELVP Check the Job Queue Status ## Example output ## Local download SPOT-peptide: Template-based prediction of peptide binding proteins and peptide binding sites /server/spot-peptide/ Wed, 15 Jan 2020 00:00:00 +0000 /server/spot-peptide/ E-mail address (optional): Target (optional): PDB File: List of PDB IDs: Input structure File MUST be in PDB format OR a list of 5-character PDB ids - ID+chain e.g. 1elrA ## Example output ## Help page SPOT-Contact: Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks /server/spot-contact-casp/ Sat, 10 Feb 2001 00:00:00 +0000 /server/spot-contact-casp/ Our resources are limited. If you wish to run several batches per day please make use of the downloadable package or contact the administrator directly. E-mail address (optional): Target (optional): Input your protein Sequences: Maximum: 10 sequences at a time, less than 750AA each (FASTA format) >Example: 6KIL_A RGSATDTAATTGTASPDEPLYVQGQTELDDVTSDNDVVLADFYADWCGPCQMLEPVVETLAEQTDAAVAKIDVDENQALASAYGVRGVPTLVLFADGEQVEEVVGLQDEDALKDLIESYTELVP Check the Job Queue Status