Search Results - "Shin, Hee Woong"

AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks by Kwon, Yongbeom, Shin, Woong-Hee, Ko, Junsu, Lee, Juyong

“…Accurate prediction of the binding affinity of a protein-ligand complex is essential for efficient and successful rational drug design. Therefore, many binding…”
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In silico structure-based approaches to discover protein-protein interaction-targeting drugs by Shin, Woong-Hee, Christoffer, Charles W., Kihara, Daisuke

“…•Characteristics of PPI drug targets and PPI inhibitors are summarized.•Databases for PPI drugs and PPI targets are reviewed.•Computational methods for…”
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Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38‐46 by Christoffer, Charles, Terashi, Genki, Shin, Woong‐Hee, Aderinwale, Tunde, Maddhuri Venkata Subramaniya, Sai Raghavendra, Peterson, Lenna, Verburgt, Jacob, Kihara, Daisuke

“…We report the performance of the protein docking prediction pipeline of our group and the results for Critical Assessment of Prediction of Interactions (CAPRI)…”
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Improved performance in CAPRI round 37 using LZerD docking and template‐based modeling with combined scoring functions by Peterson, Lenna X., Shin, Woong‐Hee, Kim, Hyungrae, Kihara, Daisuke

“…We report our group's performance for protein‐protein complex structure prediction and scoring in Round 37 of the Critical Assessment of PRediction of…”
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GalaxyDock2: Protein-ligand docking using beta-complex and global optimization by Shin, Woong-Hee, Kim, Jae-Kwan, Kim, Deok-Soo, Seok, Chaok

“…In this article, an enhanced version of GalaxyDock protein–ligand docking program is introduced. GalaxyDock performs conformational space annealing (CSA)…”
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S-Pred: protein structural property prediction using MSA transformer by Hong, Yiyu, Song, Jinung, Ko, Junsu, Lee, Juyong, Shin, Woong-Hee

“…Predicting the local structural features of a protein from its amino acid sequence helps its function prediction to be revealed and assists in…”
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Three-dimensional compound comparison methods and their application in drug discovery by Shin, Woong-Hee, Zhu, Xiaolei, Bures, Mark Gregory, Kihara, Daisuke

“…Virtual screening has been widely used in the drug discovery process. Ligand-based virtual screening (LBVS) methods compare a library of compounds with a known…”
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Human and server docking prediction for CAPRI round 30‐35 using LZerD with combined scoring functions by Peterson, Lenna X., Kim, Hyungrae, Esquivel‐Rodriguez, Juan, Roy, Amitava, Han, Xusi, Shin, Woong‐Hee, Zhang, Jian, Terashi, Genki, Lee, Matt, Kihara, Daisuke

“…ABSTRACT We report the performance of protein–protein docking predictions by our group for recent rounds of the Critical Assessment of Prediction of…”
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Discovery of a Potent Candidate for RET-Specific Non-Small-Cell Lung Cancer—A Combined In Silico and In Vitro Strategy by Ramesh, Priyanka, Shin, Woong-Hee, Veerappapillai, Shanthi

“…Rearranged during transfection (RET) is a tyrosine kinase oncogenic receptor, activated in several cancers including non-small-cell lung cancer (NSCLC)…”
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A remarkable genetic shift in a transmitted/founder virus broadens antibody responses against HIV-1 by Jain, Swati, Uritskiy, Gherman, Mahalingam, Marthandan, Batra, Himanshu, Chand, Subhash, Trinh, Hung V, Beck, Charles, Shin, Woong-Hee, Alsalmi, Wadad, Kijak, Gustavo, Eller, Leigh A, Kim, Jerome, Kihara, Daisuke, Tovanabutra, Sodsai, Ferrari, Guido, Robb, Merlin L, Rao, Mangala, Rao, Venigalla B

“…A productive HIV-1 infection in humans is often established by transmission and propagation of a single transmitted/founder (T/F) virus, which then evolves…”
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Exploring safe and potent bioactives for the treatment of non-small cell lung cancer by Thirunavukkarasu, Muthu Kumar, Shin, Woong-Hee, Karuppasamy, Ramanathan

“…Activating and suppressing mutations in the MAPK pathway receptors are the primary causes of NSCLC. Of note, MEK inhibition is considered a promising strategy…”
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LigDockCSA: Protein-ligand docking using conformational space annealing by Shin, Woong-Hee, Heo, Lim, Lee, Juyong, Ko, Junsu, Seok, Chaok, Lee, Jooyoung

“…Protein–ligand docking techniques are one of the essential tools for structure‐based drug design. Two major components of a successful docking program are an…”
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Pannorin isolated from marine Penicillium sp. SG-W3: a selective monoamine oxidase A inhibitor by Oh, Jong Min, Gao, Qian, Shin, Woong-Hee, Lee, Eun-Young, Chung, Dawoon, Choi, Grace, Nam, Sang-Jip, Kim, Hoon

“…Six compounds were isolated from Penicillium sp. SG-W3, a marine-derived fungus, and their inhibitory activities against target enzymes relating to…”
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Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches by Shin, Woong-Hee, Kumazawa, Keiko, Imai, Kenichiro, Hirokawa, Takatsugu, Kihara, Daisuke

“…Driving mechanisms of many biological functions in a cell include physical interactions of proteins. As protein-protein interactions (PPIs) are also important…”
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An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes by Chiba, Shuntaro, Ishida, Takashi, Ikeda, Kazuyoshi, Mochizuki, Masahiro, Teramoto, Reiji, Taguchi, Y-h., Iwadate, Mitsuo, Umeyama, Hideaki, Ramakrishnan, Chandrasekaran, Thangakani, A. Mary, Velmurugan, D., Gromiha, M. Michael, Okuno, Tatsuya, Kato, Koya, Minami, Shintaro, Chikenji, George, Suzuki, Shogo D., Yanagisawa, Keisuke, Shin, Woong-Hee, Kihara, Daisuke, Yamamoto, Kazuki Z., Moriwaki, Yoshitaka, Yasuo, Nobuaki, Yoshino, Ryunosuke, Zozulya, Sergey, Borysko, Petro, Stavniichuk, Roman, Honma, Teruki, Hirokawa, Takatsugu, Akiyama, Yutaka, Sekijima, Masakazu

“…We propose a new iterative screening contest method to identify target protein inhibitors. After conducting a compound screening contest in 2014, we report…”
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Three-dimensional Krawtchouk descriptors for protein local surface shape comparison by Sit, Atilla, Shin, Woong-Hee, Kihara, Daisuke

“…•2D Krawtchouk descriptors have been extended to 3D for local comparison of 3D surfaces.•The location of the region-of-interest can be controlled by changing…”
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Modeling the assembly order of multimeric heteroprotein complexes by Peterson, Lenna X, Togawa, Yoichiro, Esquivel-Rodriguez, Juan, Terashi, Genki, Christoffer, Charles, Roy, Amitava, Shin, Woong-Hee, Kihara, Daisuke

“…Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been…”
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GalaxySite: ligand-binding-site prediction by using molecular docking by Heo, Lim, Shin, Woong-Hee, Lee, Myeong Sup, Seok, Chaok

“…Knowledge of ligand-binding sites of proteins provides invaluable information for functional studies, drug design and protein design. Recent progress in…”
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55 Years of the Rossmann Fold by Shin, Woong-Hee, Kihara, Daisuke

“…The Rossmann fold is one of the most commonly observed structural domains in proteins. The fold is composed of consecutive alternating β-strands and α-helices…”
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Current progress and future perspectives of polypharmacology : From the view of non-small cell lung cancer by Karuppasamy, Ramanathan, Veerappapillai, Shanthi, Maiti, Sayoni, Shin, Woong-Hee, Kihara, Daisuke

“…A pre-eminent subtype of lung carcinoma, Non-small cell lung cancer accounts for paramount causes of cancer-associated mortality worldwide. Undeterred by the…”
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