Search Results - "Li, Zhanwen"

FATCAT 2.0: towards a better understanding of the structural diversity of proteins by Li, Zhanwen, Jaroszewski, Lukasz, Iyer, Mallika, Sedova, Mayya, Godzik, Adam

“…Abstract FATCAT 2.0 server (http://fatcat.godziklab.org/), provides access to a flexible protein structure alignment algorithm developed in our group. In such…”
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FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking by Xu, Dong, Jaroszewski, Lukasz, Li, Zhanwen, Godzik, Adam

“…Homology detection enables grouping proteins into families and prediction of their structure and function. The range of application of homology-based…”
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Stress redistribution of dynamic loading incident with arbitrary waveform through a circular cavity by Tao, Ming, Li, Zhanwen, Cao, Wenzhuo, Li, Xibing, Wu, Chengqing

“…Summary In actual geotechnical and civil engineering, dynamic stress concentrations around cavities generated by wave sources widely exist. In this study,…”
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AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction by Xu, Dong, Jaroszewski, Lukasz, Li, Zhanwen, Godzik, Adam

“…Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new…”
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Identification and validation of a novel 16-gene prognostic signature for patients with breast cancer by Zhong, Zhenhua, Jiang, Wenqiang, Zhang, Jing, Li, Zhanwen, Fan, Fengfeng

“…Despite increased early diagnosis and improved treatment in breast cancer (BRCA) patients, prognosis prediction is still a challenging task due to the disease…”
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Difference contact maps: From what to why in the analysis of the conformational flexibility of proteins by Iyer, Mallika, Li, Zhanwen, Jaroszewski, Lukasz, Sedova, Mayya, Godzik, Adam

“…Protein structures, usually visualized in various highly idealized forms focusing on the three-dimensional arrangements of secondary structure elements, can…”
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Dynamic stress state around shallow-buried cavity under transient P wave loads in different conditions by Li, Zhanwen, Tao, Ming, Du, Kun, Cao, Wenzhuo, Wu, Chengqing

“…•The theoretical model of cavity under various transient P wave loads is obtained.•Stress distributions around cavity of high and low frequency loads are…”
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Feasibility of calculating rocuronium dosage by skeletal muscle weight in patients with obesity by Hu, Zhenhua, Li, Benmu, Li, Zhanwen, Liu, Zhe, Liu, Shengqun

“…This study aimed to investigate the dose-response relationship of rocuronium administered based on skeletal muscle weight and to assess the feasibility of…”
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Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima by Zhang, Ying, Thiele, Ines, Weekes, Dana, Li, Zhanwen, Jaroszewski, Lukasz, Ginalski, Krzysztof, Deacon, Ashley M, Wooley, John, Lesley, Scott A, Wilson, Ian A, Palsson, Bernhard, Osterman, Andrei, Godzik, Adam

“…Metabolic pathways have traditionally been described in terms of biochemical reactions and metabolites. With the use of structural genomics and systems…”
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Exploration of uncharted regions of the protein universe by Jaroszewski, Lukasz, Li, Zhanwen, Krishna, S Sri, Bakolitsa, Constantina, Wooley, John, Deacon, Ashley M, Wilson, Ian A, Godzik, Adam

“…The genome projects have unearthed an enormous diversity of genes of unknown function that are still awaiting biological and biochemical characterization…”
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Ubiquitin-Specific Peptidase USP22 Negatively Regulates the STAT Signaling Pathway by Deubiquitinating SIRT1 by Ao, Ning, Liu, Yanyan, Feng, Hailiang, Bian, Xiaocui, Li, Zhanwen, Gu, Bei, Zhao, Xiaomei, Liu, Yuqin

“…Background/Aims: The ubiquitin-specific peptidase USP22 mediates various cellular and organismal processes, such as cell growth, apoptosis, and tumor…”
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Structural Determinants of Limited Proteolysis by Kazanov, Marat D, Igarashi, Yoshinobu, Eroshkin, Alexey M, Cieplak, Piotr, Ratnikov, Boris, Zhang, Ying, Li, Zhanwen, Godzik, Adam, Osterman, Andrei L, Smith, Jeffrey W

“…Limited or regulatory proteolysis plays a critical role in many important biological pathways like blood coagulation, cell proliferation, and apoptosis. A…”
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Using an alignment of fragment strings for comparing protein structures by Friedberg, Iddo, Harder, Tim, Kolodny, Rachel, Sitbon, Einat, Li, Zhanwen, Godzik, Adam

“…Motivation: Most methods that are used to compare protein structures use three-dimensional (3D) structural information. At the same time, it has been shown…”
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Trend of ambient seismic noise attenuation tomography: Theory and applications by Liu, Xin, Li, Zhanwen

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Dynamic stress concentration and failure characteristics around elliptical cavity subjected to impact loading by Tao, Ming, Zhao, Rui, Du, Kun, Cao, Wenzhuo, Li, Zhanwen

“…Wave function expansion method is used to solve the scattering and dynamic stress concentration around the elliptic cavity in the full plane under steady state…”
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ModFlex: Towards Function Focused Protein Modeling by Sedova, Mayya, Jaroszewski, Lukasz, Iyer, Mallika, Li, Zhanwen, Godzik, Adam

“…[Display omitted] •Homology modeling method uses known protein structures as templates.•Templates are often chosen based on their sequence identity to the…”
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PDBFlex: exploring flexibility in protein structures by Hrabe, Thomas, Li, Zhanwen, Sedova, Mayya, Rotkiewicz, Piotr, Jaroszewski, Lukasz, Godzik, Adam

“…The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as…”
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POSA: a user-driven, interactive multiple protein structure alignment server by Li, Zhanwen, Natarajan, Padmaja, Ye, Yuzhen, Hrabe, Thomas, Godzik, Adam

“…POSA (Partial Order Structure Alignment), available at http://posa.godziklab.org, is a server for multiple protein structure alignment introduced in 2005…”
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Blood transfusion and risk of atrial fibrillation after coronary artery bypass graft surgery: A meta-analysis of cohort studies by Liu, Shengqun, Li, Zhanwen, Liu, Zhe, Hu, Zhenhua, Zheng, Gaifang

“…The aim of this study was to systematically evaluate the effect of blood transfusion (BT) on postoperative atrial fibrillation (AF) in adult patients who had…”
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AIDA: ab initio domain assembly server by Xu, Dong, Jaroszewski, Lukasz, Li, Zhanwen, Godzik, Adam

“…AIDA: ab initio domain assembly server, available at http://ffas.burnham.org/AIDA/ is a tool that can identify domains in multi-domain proteins and then…”
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