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Computational screening of novel enzymes using ocr-based protein fingerprint
( Amit Goyal ),황규석,이선구 한국공업화학회 2016 한국공업화학회 연구논문 초록집 Vol.2016 No.0
Design of an efficient fingerprint that detects homologous proteins at distant sequence identity has been a great challenge. We have developed a strategy to extract an ideal-like fingerprint with high specificity and sensitivity from a group of sequences related to a fold. The fingerprint was generated by selecting the overlapped conserved residues (OCR) from the conserved residues of homologous proteins obtained using independent three alignment methods, i.e. multiple sequence alignment, structure-based alignment, and alignment based on the interstrand hydrogen-bonds. The OCR-based fingerprints were tested on protein folds of various classes with discrete sequence similarities, and showed more than 90% detection efficiency for all the folds tested. Finally, the approach was employed in the computational screening of novel enzymes such as Cupredoxin proteins and Cytochrome P450 proteins from protein sequence database.
Identification of Novel Cytochrome P450 Homologs Using Overlapped Conserved Residues Based Approach
Amit Goyal,김병지,황규석,이선구 한국생물공학회 2015 Biotechnology and Bioprocess Engineering Vol.20 No.3
Cytochrome P450 enzymes are one of the most versatile biological catalysts that are found in nature. They have potentials as a drug target in pharmaceutical industries, as a biocatalyst in bioconversion process in chemical industries, and as a biosensor in biomedical industries. Proteins in CYPs superfamily are closely related in structural and functional properties but share low sequence similarity, which makes the identification and characterization of the novel P450 homologs a challenging task. In this study, the overlapped conserved residue (OCR) based approach was used to identify the fingerprints for the alpha-helical rich CYPs, and they were tested to detect novel P450 homologs in the NCBI non-redundant protein sequence database. We could identify 13 potential novel P450 sequence homologs, which were validated at the sequence and structural levels for the presence of the conserved PROSITE motif and conserved Cytochrome P450 structure domain, respectively. This study suggests that the OCR-based approach can be a useful way to detect novel homologous α-helix rich proteins such as Cytochrome P450s.
Identification of Novel Cupredoxin Homologs Using Overlapped Conserved Residues Based Approach
( Amit Goyal ),( Bharat Madan ),( Kyu Suk Hwang ),( Sun Gu Lee ) 한국미생물 · 생명공학회 2015 Journal of microbiology and biotechnology Vol.25 No.1
Cupredoxin-like proteins are mainly copper-binding proteins that conserve a typical rigid Greek-key arrangement consisting of an eight-stranded β-sandwich, even though they share as little as 10-15% sequence similarity. The electron transport function of the Cupredoxins is critical for respiration and photosynthesis, and the proteins have therapeutic potential. Despite their crucial biological functions, the identification of the distant Cupredoxin homologs has been a difficult task due to their low sequence identity. In this study, the overlapped conserved residue (OCR) fingerprint for the Cupredoxin superfamily, which consists of conserved residues in three aspects (i.e., the sequence, structure, and intramolecular interaction), was used to detect the novel Cupredoxin homologs in the NCBI non-redundant protein sequence database. The OCR fingerprint could identify 54 potential Cupredoxin sequences, which were validated by scanning them against the conserved Cupredoxin motif near the Cu-binding site. This study also attempted to model the 3D structures and to predict the functions of the identified potential Cupredoxins. This study suggests that the OCR-based approach can be used efficiently to detect novel homologous proteins with low sequence identity, such as Cupredoxins.
A Review on Air Quality Indexing System
Kanchan,Amit Kumar Gorai,Pramila Goyal 한국대기환경학회 2015 Asian Journal of Atmospheric Environment (AJAE) Vol.9 No.2
Air quality index (AQI) or air pollution index (API) is commonly used to report the level of severity of air pollution to public. A number of methods were developed in the past by various researchers/environmental agencies for determination of AQI or API but there is no universally accepted method exists, which is appropriate for all situations. Different method uses different aggregation function in calculating AQI or API and also considers different types and numbers of pollutants. The intended uses of AQI or API are to identify the poor air quality zones and public reporting for severity of exposure of poor air quality. Most of the AQI or API indices can be broadly classify as single pollutant index or multi-pollutant index with different aggregation method. Every indexing method has its own characteristic strengths and weaknesses that affect its suitability for particular applications. This paper attempt to present a review of all the major air quality indices developed worldwide.
A Review on Air Quality Indexing System
Kanchan, Kanchan,Gorai, Amit Kumar,Goyal, Pramila Korean Society for Atmospheric Environment 2015 Asian Journal of Atmospheric Environment (AJAE) Vol.9 No.2
Air quality index (AQI) or air pollution index (API) is commonly used to report the level of severity of air pollution to public. A number of methods were developed in the past by various researchers/environmental agencies for determination of AQI or API but there is no universally accepted method exists, which is appropriate for all situations. Different method uses different aggregation function in calculating AQI or API and also considers different types and numbers of pollutants. The intended uses of AQI or API are to identify the poor air quality zones and public reporting for severity of exposure of poor air quality. Most of the AQI or API indices can be broadly classify as single pollutant index or multi-pollutant index with different aggregation method. Every indexing method has its own characteristic strengths and weaknesses that affect its suitability for particular applications. This paper attempt to present a review of all the major air quality indices developed worldwide.
Selvakumar Edwardraja,Ganapathiraman Munussami,Amit Goyal,이선구 한국생물공학회 2016 Biotechnology and Bioprocess Engineering Vol.21 No.6
There is a considerable interest in the detection of GFP-like proteins due to their structural stability and functional usefulness. GFP-like proteins share highly conserved beta-barrel fold with 11 beta-strands. However, their low sequence identity hampers efficient identification of their homologous proteins from database. In this study, an attempt was made to generate a fingerprint for efficient detection of GFP-like proteins. Overlapped conserved residues (OCR)-based approach has been used to design a protein fingerprint based on sequentially and structurally conserved residues in secondary structures to detect homologous proteins very efficiently. Therefore, a fingerprint for GFP-like fold was designed using the OCR approach. However, its specificity was too low to be used for the identification of novel proteins. The conserved residues of loop regions were added and optimized to improve its specificity without losing its high sensitivity. The optimized fingerprint was employed to scan NR database. A total of 20 hypothetical proteins were detected, among which nine were validated as potential GFP-like homologs.
Sharma Vivek Mohan,Mathur Amit,Goyal Mohan Babu,Jat Shankar Lal 소화기인터벤션의학회 2023 International journal of gastrointestinal interven Vol.12 No.2
Background: Post-endoscopic retrograde cholangiopancreatography pancreatitis (PEP) is a common complication of therapeutic endoscopy. The aim of this trial was to determine whether a combination of rectal diclofenac and vigorous hydration with Ringer’s lactate is superior to the correspond-ing individual treatments for preventing PEP in high-risk patients. Methods: This randomized, open-label, controlled trial was conducted from August 2020 to January 2022. We included patients who were at high risk of developing PEP. Three intervention groups were made: group A, diclofenac sodium suppository (100 mg); group B, aggressive hydration with Ringer’s lactate; group C, a combination of diclofenac and aggressive hydration. PEP was defined as a serum amylase level > 3 times the upper limit of normal with epigastric pain within 24 hours after endoscopic retrograde cholangiopancreatography.Results: A total of 144 patients were included and 48 cases were randomized to each intervention group. The incidence of PEP was 8.3%, 10.4%, and 8.3% in groups A, B, and C, respectively. A personal history of alcohol consumption and more than one pancreatic duct guidewire cannulation were significantly associated with the development of PEP.Conclusion: No difference in the incidence of PEP was observed with or without the use of aggressive hydration. Combining aggressive hydration with a rectal nonsteroidal anti-inflammatory drug for preventing PEP cannot be recommended.