Utilizing random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server

Lee, Kyoungyeul,Lee, Minho,Kim, Dongsup BioMed Central 2017 BMC bioinformatics Vol.18 No.suppl16

<P><B>Background</B></P><P>The identification of target molecules is important for understanding the mechanism of “target deconvolution” in phenotypic screening and “polypharmacology” of drugs. Because conventional methods of identifying targets require time and cost, <I>in-silico</I> target identification has been considered an alternative solution. One of the well-known <I>in-silico</I> methods of identifying targets involves structure activity relationships (SARs). SARs have advantages such as low computational cost and high feasibility; however, the data dependency in the SAR approach causes imbalance of active data and ambiguity of inactive data throughout targets.</P><P><B>Results</B></P><P>We developed a ligand-based virtual screening model comprising 1121 target SAR models built using a random forest algorithm. The performance of each target model was tested by employing the ROC curve and the mean score using an internal five-fold cross validation. Moreover, recall rates for top-<I>k</I> targets were calculated to assess the performance of target ranking. A benchmark model using an optimized sampling method and parameters was examined via external validation set. The result shows recall rates of 67.6% and 73.9% for top-11 (1% of the total targets) and top-33, respectively. We provide a website for users to search the top-<I>k</I> targets for query ligands available publicly at http://rfqsar.kaist.ac.kr.</P><P><B>Conclusions</B></P><P>The target models that we built can be used for both predicting the activity of ligands toward each target and ranking candidate targets for a query ligand using a unified scoring scheme. The scores are additionally fitted to the probability so that users can estimate how likely a ligand–target interaction is active. The user interface of our web site is user friendly and intuitive, offering useful information and cross references.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (10.1186/s12859-017-1960-x) contains supplementary material, which is available to authorized users.</P>

곰소만 어촌의 어로활동에 관한 민족지적 연구: 1970년대 이후 어업의 변화를 중심으로

조숙정 서울대학교 비교문화연구소 2017 비교문화연구 Vol.23 No.2

This paper examines fishery changes of a fishing village in Gomso Bay ethnographically to understand the changes of local fishing from local fishermen’s experience. Firstly this paper describes one-year- period fishing activities. Then the changes of the fishery and the village from 1970’s to the early 2010’s are discussed in three dimensions of fishing area, fishing equipment and technique, and fishing targets. The fishery of the village in the Bay changed greatly in the mid 1970’s, and the depletion of coast marine resources was getting worse. The significant changes are the motorization of fishing boats, the introduction of nylon fishing nets, the development of new species of fish caught, and the expansion into the open sea. It is remarkable that the farming and fishing village in the past became functionally the full-time fishing village. 본고는 곰소만 연안어촌의 민족지적 사례를 통해 서해 조기잡이가 쇠퇴 하는 1970년대 이후 어업의 주요 변화를 미시적 관점에서 기술 · 분석한 것이다. 그럼으로써 어민들의 입장에서 중요하게 경험된 어로활동의 변화 가 무엇인지를 이해해 보고자 했다. 먼저 조사지 어촌의 1년 주기 어로활동 을 계절별 · 어장별로 기술함으로써, 현재 어민들이 종사하고 있는 어로활 동의 양상을 살펴본다. 이를 토대로 어민들이 강조하여 설명하는 어업 변 화를 어로공간, 어구어법, 어로대상이라는 세 가지 차원에서 살펴본다. 조 사지에서는 1970년대 중반에 어선의 동력화와 나일론그물이 도입되었고 새로운 어장이 개발되는 등 커다란 변화가 있었다. 곰소만과 위도 앞바다에 서 1톤급 풍선을 타고 조기 · 갈치 등을 주낙으로 잡던 어민들은 오늘날 1~2 톤급 선외기 어선과 그물·통발로 꽃게·주꾸미 등을 잡는 어업에 종사하고 있다. 그리고 1980~90년대에 양식어촌과 관광어촌의 기능을 가졌던 조사 지는 2000년대 중반 이후 오히려 어선어업 중심의 순수 어로어촌으로 기능 이 더욱 강화된 양상이다.

쏨뱅이의 체장 및 유영자세각에 따른 음향반사강도

지유근(Yu-Geun JI),심규경(Kyu-Kyeong SHIM),송건우(Keon-Woo SONG),윤은아(Eun-A YOON),황두진(Doo-Jin HWANG) 전남대학교 어업기술연구소 2016 어업기술연구소보고지 Vol.9 No.1

Scorpion fish Sebastiscus marmoratus are hatched and released in marine ranching areas in Korea to assist in the recovery and management of fishery resources in coastal areas. Information on the acoustic target strength (TS) of marine organisms in order to convert volume backscattering strength into estimates of biomass. The aim of this study were TS of scorpion fish. The TS was measured in acoustic seawater tank (5 m (L)×5 m (H)×5 m (D)) at the fisheries science institute of Chonnam National University, Korea. Acoustic data was collected with a 200 kHz quantitative echo sounder (dual-beam, BioSonics). Behavior of scorpion fish was observed underwater camera installed side and bottom in tank. Acoustic and behavior data were synchronized intervals of 0.5 sec. The scorpion fish ranged from 14.0 to 26.0 cm in length and from 40 to 310g in wet weight. The relationships between and fish total length were as follows: TSmax.=20 log (TL)‑69.22 and TSavg.=20 log (TL)‒73.8. This result will be provided basic information for conducting acoustic survey of the scorpion fish.

산지하천에 설치된 계단식 전석 어도의 수리 특성 분석

김기흥 한국수자원학회 2022 한국수자원학회논문집 Vol.55 No.1

This study was intended to suggest the applicability of stepped boulder fishway using the concept of traditional boulder weir, focusing on the problems of existing concrete pool-and-weir fishways installed in mountain streams. To achieve this purpose, a stepped boulder fishway was designed and constructed as a pilot project in consideration of ascending capacity of the selected target fishes. Under the given discharge conditions, the hydraulic characteristics of the fishway were investigated in the field, and the characteristics and ascending capacity of the fishes were compared and analyzed. The fishway had a short length and steep slope, but the mean drops between each baffle were the range of 0.15 to 0.29 m, and this range satisfied the limit condition of about 0.40 m, which was in the limit of the drop that target fishes can ascend. The mean velocities of each baffle and pool were 0.82 to 0.87 m/sec and 0.13 to 0.24 m/sec. This result satisfied the conditions of burst speed (10 to 30 times of body length) and mean velocity of the resting pool (7 to 25% of burst speed) for target fishes. Since the bottom surface of the pool formed of boulders had a gentle reverse slope and rotational flow did not occur, the efficiency of fishway can be increased, and it will also be possible to solve the maintenance problem by flushing bed materials. 본 연구는 산지하천에 설치된 기존의 콘크리트 계단식 어도의 문제점에 착안하여 전통적인 돌보의 개념을 응용한 계단식 전석 어도의 적용성을 제시하고자 하였다. 이러한 목적을 달성하기 위해 선정된 대표어종의 소상능력을 고려하여 계단식 전석 돌보를 설계, 시공하였다. 현장측정을 통하여 주어진 유량조건 하에서 어도의 수리특성을 조사하고 대표어종의 소상능력과 비교, 분석하였다. 어도의 길이가 짧고 급경사인 구조이지만, 각 배플 사이의 평균낙차가 0.15~0.29 m 범위였으며, 이 범위는 대표어종이 소상할 수 있는 낙차의 한계조건인 약 0.40 m를 만족시킬 수 있었다. 각 배플과 풀의 평균유속은 0.82~0.87 m/sec와 0.13~0.24 m/sec 이었다. 이 결과는 대표어종이 소상 가능한 돌진속도(체장의 10~30 배)와 휴식처 평균유속(돌진속도의 7~25%)의 조건을 충족시켰다. 전석으로 형성된 풀의 바닥면이 완만한 역경사면으로 되어 회전류가 발생하지 않기 때문에 어도의 효율을 증가시킬 수 있고, 또한 토사퇴적을 차단하여 어도의 유지관리 문제점을 해소할 수 있을 것이다.

한국 남해안 부어류의 음향반사강도에 관한 연구 I. 멸치 (Engraulis japonica)의 in situ 반사강도 측정

윤갑동,김장근,최영민,YOON Gab Dong,KIM Zang Geun,CHOI Young Min 한국수산과학회 1996 한국수산과학회지 Vol.29 No.1

우리나라 연안에 분포되어 있는 주요 어업대상어종의 자원량을 측정하기 위한 기초자료를 얻기 위하여 남해동부연안에 분포하는 멸치어군을 대상으로 Split beam 어군탐지기를 이용하여 in situ TS를 측정한 결과를 요약하면 다음과 같다. 1. 본 조사에서 어획물의 $95\%$가 멸치였으며, 그 체장빈도 분포는 체장범위 $13.6\~15.4cm$, 평균체장 14.4cm이었고, 체중빈도 분포는 체중범위 $16\~28g$ 평균체중 21.9 g이었다. 2. 멸치의 반사강도는 수심 $10\~30m$ 에서 $-40.7\~-69.2dB,\;30\~50m$, 수층에서 $-42.2\~-67.7dB,\;10\~50m$ 수층에서 $-42.2\~-67.7dB$의 범위였고, 그 빈도분포에는 2개의 mode가 명확하게 분리되어 나타났다. 3. 멸치의 평균반사강도는 -49.7 dB/fish 및 -33.1 dB/kg 이었으며, $90\%$ 신뢰구간은 1 dB 이하였다. 또한, 멸치의 반사강도 (TS)와 체장 (cm)과의 관계는 다음과 같았다. TS=20 log L-72.9. The in situ target strength for the anchovy (Engraulis japonica) were measured by the split beam echo sounder system at 38 kHz. This study allowed us to detect the single echos from anchovy shoals which were dispersed during trawling operation in day time. The results of our study were as fellows: We found that the anchouy occupied about $95\%$ of the total catch from the detected shoals from which target strength data were collected. Length distribution of anchovy showed a mode and ranged from 13.6 to 15.4cm with a mean of 14.4cm and a standard deviation of 0.45cm, and weight distribution showed a mode and ranged from 16 to 28 g witha mean of 21.9 g and a standard deviation of 2.7 g. The target strength distribution of anchovy ranged from -40.7 dB to -69.2 dB in the water layer of ,$10\~30\;m$ -42.19 to -67.7 dB in the $30\~50\;m$ and -42.2 to -67.7 dB in $10\~50\;m$, showing 2 modes in each layer, respectively. Overall mean target strengths were -49.7 dB/fish and -33.1 dB/kg, averaged by area backscattering cross section $(\sigma)$, and the confidence interval for target strength was less than 1 dB. With the mean total length and the mean target strength, we drived the target strength-length relationship as $TS(\sigma)=20\;Log\;L-72.9$.

70 및 120kHz에서 쥐노래미와 감성돔에 대한 음향 반사 강도의 체장 의존성

이대재 ( Dae Jae Lee ) 한국어업기술학회 2012 수산해양기술연구 Vol.48 No.2

Black porgy and fat greenling are commercially important fish species due to the continuously increasing demand in Korea. When estimating acoustically the fish length by a fish sizing echo sounder, it is of crucial importance to know the target strength (TS) to length dependence. In relation to these needs, the target strength experiments for live fishes were conducted in an acrylic salt water tank using two split-beam echo sounders operating at 70 and 120kHz. The target strength under well-controlled laboratory conditions was simultaneously measured with the swimming movement by digital video recording (DVR) system and analyzed as a function of fish length (L) and frequency (or wavelength l). Equations of the form TS-alog (L)+blog (l)+c were derived for their TS-length dependence. The best fit regression of TS on fork length for black porgy was TS〓20.62 log (L, m)-0.62 log (l, m)-30.68 (r 2〓0.77). The best fit regression of TS on fork length for fat greenling was TS〓12.06 log (L, m)-5.85 log (l, m)-22.15 (r 2〓0.44).

어촌체험마을 방문객 유형화에 관한 연구 - 충남 태안군 어촌체험마을을 중심으로 -

김종화 ( Jong Hwa Kim ),조은정 ( Eun Jung Cho ) 한국농촌계획학회 2014 농촌계획 Vol.20 No.3

This study classifies the types of visitors to experiential fishing villages and analyses the features and target marketing strategies by categorical groups. Seven factors are extracted by Factor Analysis and the results of Cluster Analysis indicate the classification of five groups. The first group puts emphasis on the family connection, so family centered facilities and programs are necessary. The second group is composed of surrounding area residents whose purpose of visit is unclear. So environmentally friendly village development programs to encourage local patriotism are necessary. The third group puts emphasis on the necessary facilities and programs for experiencing the fishing village and traditional play, etc. The fourth group emphasizes programs related with the region and the means to satisfy visitor’s aesthetic desires. Finally, the fifth group aims at various desires that are generally felt in experiential fishing villages. So this group requires marketing strategies from the public point of view. The existing research mostly surveys rural tourism villages, but this study highlights the difference in dealing with fishing villages as opposed to rural villages, from the perspective of industry and settlement.

한국 서해 태안해역에서의 유어 낚시용 인공어초어장 개발

김창길(Chang-Gil Kim),김병균(Byung-Gyun Kim),최용석(Yong-Suk Choi),최기호(Ki-Ho Choi),김호상(Ho-Sang Kim),김재우(Jae-Woo Kim) 한국마린엔지니어링학회 2010 한국마린엔지니어링학회 학술대회 논문집 Vol.2010 No.4

Target fish species and the oceanographic conditions are important factors for the design of an artificial reef. These factors in this study were analyzed using a Questionnaire on recreational fishing in the Taean waters. According to the results. fish species caught by recreational anglers at artificial reefs in Teaan coastal waters were chiefly Sebastes schlegeli, Hexagrammos otakii and Perslichthys olivaceus. Also, current are relatively strong. These results mean that the artificial reef for recreational fishing should be made by the combination of frame and face structure.

Unraveling the Potential Anti-Severe Acute Respiratory Syndrome Coronavirus 2 Mechanisms of Ginger by Computational Target Fishing

ShaoJun Chen,LiHua Zhang 한국식품영양과학회 2023 Journal of medicinal food Vol.26 No.10

Ginger (Zingiber officinale) is one of the most commonly consumed botanical foods. Owing to its antiinflammatoryand antiviral properties, ginger has been widely used as a homemade remedy during the corona virus disease2019 (COVID-19) pandemic; however, the mechanisms of its therapeutic activities against severe acute respiratory syndromecoronavirus 2 (SARS-CoV-2) remain obscure. In this study, we used a drug-likeness approach to screen the active compoundsof ginger. Next, we identified candidate targets of active compounds responsible for the anti-SARS-CoV-2 effects of gingerusing chemical similarity searching and SARS-CoV-2-human protein–protein interaction (PPI) data. Finally, we analyzedPPIs, Gene Ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes pathway enrichment of the candidateproteins using different bioinformatics tools. A network comprising ginger compounds, human proteins, and SARS-CoV-2proteins was built through Cytoscape 3.3. The results indicate that the anti-SARS-CoV-2 activity of ginger involves 20 activecompounds, 18 potential human targets, and 12 SARS-CoV-2 proteins. These form a pharmacological network in which sigmanonopioid intracellular receptor 1 (SIGMAR1) and histone deacetylase 2 may be druggable hub proteins. In addition,molecular docking showed that 8-gingerdione and dihydrocapsaicin may preferentially interact with SIGMAR1, which wasconfirmed by further molecular dynamics simulation (150 ns) experiments. In conclusion, ginger targets multiple humanproteins and affects multiple SARS-CoV-2 proteins to exert anti-COVID-19 effects. Although further experimental verificationis needed, this study provides a quick visual overview of the anti-SARS-CoV-2 action of ginger.

2023년 울릉군 연안바다목장 수산자원량 추정 연구

김광복,최상학,최창근 한국조류학회I 2024 수생생물 Vol.4 No.1

우리나라의 바다목장은 수산자원의 회복과 효율적인 관리를 목적으로 통영을 시작으로 전국 각 해역에 생성되었다. 수산자원을 효율적으로 관리하려면 바다목장의 정확한 상태를 파악해야 하고, 이를 위해 우선 수산자원의 현존량을 파악하고자 하였다. 수산자원의 현존량을 파악하는 방법은 여러 가지가 있으며, 그 중 어구 조사는 종 명확성은 있으나 많은 조사 시간이 필요하고, 넓은 해역의 일부 정점만 조사가 가능하므로 정량적인 조사가 어렵고, 수중음향 조사는 단시간에 넓은 해역에 서식하고 있는 어류의 시 ․ 공간적인분포 및 현존량을 평가할 수 있어 수산 선진국에서 많이 이용되고 있는 방법이다. 수중음향 조사기법은 조사해역의 우점 어류의 음향산란강도(Target strength, TS)와 현장조사를 통한 체적후방산란강도(Volume back scattering strength SV)를 기반으로 수산자원 현존량을 파악할 수 있다. 본 조사에서는 어구를 이용하여 어종을 파악하고, 수중음향 조사기법을 이용하여 연안 바다목장에 서식하는 수산자원의 어류의 밀도 및 현존량을 파악하였다. Korea’s marine ranches have been established in various coastal areas, starting with Tongyeong, with the aim of restoring and efficiently managing fishery resources. Effective management of the fishery can only be carried out if the exact status of the marine ranch is known. There are a number of different methods used to estimate the abundance of fishery resources. Of these, fishing gear surveys provide species specificity but require a lot of survey time, and quantitative surveys are difficult because only a few stations can be surveyed over a large area. On the other hand, hydroacoustic surveys are widely used in developed fisheries. They can estimate the spatial and temporal distribution and abundance of fish over large areas in a short time. Hydroacoustic surveys can estimate the abundance of fishery resources based on the target strength (TS) of dominant species in the survey area and the volume backscattering strength (SV) obtained from field surveys. In this study, fish species were identified using fishing gear and distribution and abundance of fish were estimated using hydroacoustic surveys at Ullueng coastal marine ranching area