3000 citations achieved from 35 SCI journal papers and 3 non-SCI papers (Sept 23, 2020)

Our lab obtained the US patent of “(US20190183860) METHOD FOR THE TREATMENT OF ATG4-RELATED DISORDERS”

Application Number: 15842910 Application Date: 15.12.2017
Publication Number: 20190183860 Publication Date: 20.06.2019
Applicants: National Tsing Hua University
Inventors: Lee-Wei Yang
Chih-Wen Shu
Pei-Feng Liu
Kun-Lin Tsai

本實驗室獲得ATG4相關抗癌藥物之美國專利! (Dec 2019)

Our New Publication on Linear Response Theory ( ); the work is also in honor of the contribution of Prof Nobuhiro Go to the Progress of Theoretical and Computational Biophysics (Nov 2019)

Congratulations to our another linear response theory paper getting accepted – Bang-Chieh Huang (our former postdoc) and Lee-Wei Yang (2019) Molecular dynamics simulations and linear response theories jointly describe biphasic responses of myoglobin relaxation and reveal evolutionarily conserved frequent communicators. (accepted by Biophysics and Physicobiology; a special issue to honor Nobuhiro Gō sensei’s contribution to Biophysics Society and his 80 year old birthday) bioRxiv (Sept 2019)

Congratulations to Dr Justin Chan for his latest first-author publication accepted by Structure –  Justin Chan, Hong-Rui Lin, Kazuhiro Takemura, Kai-Chun Chang, Yuan-Yu Chang, Yasumasa Joti, Akio Kitao, Lee-Wei Yang* (2019) “An efficient timer and sizer of biomacromolecular motions”. Structure (accepted; preprint(Sept 2019) 

Congratulations to Mr Kevin Chen (陳柏淳) for passing the oral defense for his Master degree and thesis entitled “A novel software to predict the -1 Programmed Ribosomal Frameshifting (-1PRF) signals in viral genomes –predicted signals are validated by cell-free bioassays for Zika virus genome”  !  (July 2019)

Congratulations to Dr-to-be Justin Chan for winning the best student oral presentation award in 2019 Computational Biology Workshop held by National Center for Theoretical Sciences (NCTS) as well as his first-author publication accepted by Bioinformatics –  Justin Chan, Jinhao Zou, Christopher Llynard Ortiz, Chi-Hong Chang Chien, Rong-Long Pan, Lee-Wei Yang* (2019) DR-SIP: Protocols for Higher Order Structure Modeling with Distance Restraints- and Cyclic Symmetry-Imposed Packing. Bioinformatics (accepted) (July 2019)

Congratulations to Mr Kun-Wei Lin  (林昆衛) in receiving the Merit Award in 2019 Graduate Student Symposium in the College of Life Science, NTHU (Cash award/優勝獎金:5,000 NTD)   (May 2019)

Our China patent for “Evaluation system for the efficacy of antimicrobial peptides and the use thereof” has been approved.
本實驗室獲得中國專利核准通過 CN106469251A
國別/類別:中國 / 發明專利
代 理 人:北京元本知識產權代理事務所

另一分案專利也已公開 CN109535226A  (Apr 2019)

Congratulations to Yang lab for being awarded 48,000 node-hours computation resources by High Performance Computing Infrastructure (HPCI), Japan, for the year 2019-2020! (Feb 2019)

Congratulations to Mr Kevin Chen (陳柏淳) in receiving scholarship for entering the accelerated Master program (預研生入學獎學金:每名10,000元及獎狀乙紙) !  (Sept 2018)

Congratulations to Dr Kai-Chun Chang, Mr Emmanuel O Salawu (co-first author) and Mr Yuan-Yu Chang for their latest publication in Bioinformatics – Kai-Chun Chang* , Emmanuel Oluwatobi Salawu, Yuan-Yu Chang, Jin-Der Wen and Lee-Wei Yang* (2018) Ribosomal frameshifting is a consequence of force-induced subunit rolling.  Bioinformatics. (published; IF: 7.3; ranked 3/59 in Mathematical & Computational Biology) (Aug 2018)

Congratulations to Mr Kun-Wei Lin (林昆衛) who was awarded the undergraduate research fund provided by Life Science College, NTHU (30,000 NTD a year); 恭喜 Mr 林昆衛 之研究專題「結合模擬與實驗以跨分子異構調控的方式來下調細胞自噬蛋白之活性進而抑制癌細胞的生長」獲得107學年清華大學生命科學院獎勵大學生進行專題研究計畫獲補助  (Aug 2018)

Congratulations to Mr Kun-Lin Tsai for winning the Scholarship (20,000 NTD) from Shen’s Culture & Education Foundation (沈巨塵先生清華獎學金-論文發表獎勵金) for his recent publication on Theranostics ( Dec, 2017) !

Congratulations to Ms Jinhao Zou who had her first paper accepted – Imran Khan, Yu-Kai Su, Jinhao Zou, Lee-Wei Yang, Ruey-Hwang Chou* and Chin Yu* (2017) S100B as an antagonist to block the interaction between S100A1 and the RAGE V domain. PLOS ONE, 13(2):e0190545 (accepted Dec, 2017; published Feb, 2018)

Congratulations to Mr Kun-Lin Tsai (co-first author) for his second publication from this lab – Pei-Feng Liu†; Kun-Lin Tsai†; Chien-Jen Hsu; Wei-Lun Tsai; Jin-Shiung Cheng; Hsueh-Wei Chang; Chung-Wai Shiau; Yih-Gang Goan; Ho-Hsing Tseng; Chih-Hsuan Wu; John C. Reed; Lee-Wei Yang*; Chih-Wen Shu*(2017) Drug Repurposing Screening Identifies Tc as an ATG4 Inhibitor that Suppresses Autophagy and Sensitizes Cancer Cells to Chemotherapy, Theranostics 8, 830-845 (IF = 8.8; rank 8/128 in Medicine, Research & Experimental)(Dec, 2017)

Congratulations to Mr Yuan-Yu Chang who just won the Scholarship (20,000 NTD) from Shen’s Culture & Education Foundation (沈巨塵先生清華獎學金-論文發表獎勵金) for his publication – “DynOmics: dynamics of structural proteome and beyond. Nucleic Acids Research (2017)” (June, 2017)

Congratulations to Ms Jinhao (Jane) Zou who won the honorable mention (佳作) and cash prize 2000 NTD in 2017 College of Life Science Graduate Student Symposium, NTHU (June 2nd, 2017)

Congratulations to Mr Justin Chan won the second place in the poster/oral presentation competition in the 22nd Biophysics Conference, Taiwan. Mr Yuan-Yu Chang were selected to be one of the best poster presenters. (May 2017) (Group A)

Congratulations to Mr Yuan-Yu Chang (co-first author) for his fourth publications from this lab – Hongchun Li†, Yuan-Yu Chang†, Ji Young Lee, Ivet Bahar* and Lee-Wei Yang* (2017). DynOmics: Dynamics of Structural Proteome and Beyond. Nucleic Acids Research. 45, W374–W380 (IF: 9.2; Rank 18/289 in Biochemistry & Molecular Biology)(Apr 2017) ; Listed as one example of the graphical abstracts by NAR – &     being the first paper mentioned in its category –

US & China patent publication ( (Mar 2017)

Congratulations to Mr Chris Lo (co-first author) and Mr Yuan-Yu Chang for their first and third publications from this lab – Jui-Chieh Yin, Chun-Hsien Fei, Yen-Chen Lo, Yu-Yuan Hsiao, Jyun-Cyuan Chang, Jay C Nix, Yuan-Yu Chang, Lee-Wei Yang*, I-Hsiu Huang*, Shuying Wang* (2016, Nov) Structural insights into substrate recognition by Clostridium difficile sortase. Frontiers in Cellular and Infection Microbiology. (IF: 5.2; Rank 18/123 in Microbiology)(Nov 2016)

We obtained the first preliminary approval of our China patent (中國 / 發明專利專利名稱:评估抗菌肽抗菌力的系统及其使用方法申請日期:2016.08.17 申請案號:201610682437.7 申請人:楊立威   代理人:北京元本知識產權代理事務所 審查人員:李煒倩) (Oct 2016)

Congratulations to Mr Kun-Lin Tsai in obtaining Chancellor’s Scholarship (校長獎學金; 25,000NT/month) for 4 years to support his PhD study! (Oct 2016)

Congratulations to Aravind and Justin’s recent publication in Journal of Chemical Theory and Computation – Chandrasekaran, Aravind, Chan, Justin, Lim, Carmay*, Yang, Lee-Wei* (2016) Protein dynamics and contact topology reveal protein-DNA binding orientation. Journal of Chemical Theory and Computation doi:10.1021/acs.jctc.6b00688 (5-year impact factor: 5.8; Ranking: 5/35 in Atomic, Molecular & Chemical Physics) (Sept 2016).

We obtained the first Taiwan patent on computational evaluation system for the efficacy of antimicrobial peptide (Sept 2016)!

證書號/公告號 I557587  公開號 201709097  國別/類別:中華民國 / 發明專利 專利名稱:評估抗菌胜肽之抗菌力之系統及其使用方法 申請日期:2015.08.17 申請案號:104126710 申 請 人:國立清華大學 發 明 人:楊立威、程家維、李紅春、蔡政育、游輝元 代 理 人:王正利 審查人員:謝進忠

Congratulations to Mr Kevin Chen (陳柏淳) in receiving College Research Support in 2016 (105學年度清華大學生命科學院獎勵大學生進行專題研究計畫獲補助) for the ZIKA virus related research, entitled “以生物資訊、電腦模擬、單分子光鉗以及cell-free系統來偵測Zika病毒的框架移轉(ribosomal frameshift)位置,偽節(pseudoknot)的二級結構及其機械抗力”!  (Sept 2016)

Congratulations to Mr Kun-Lin Tsai’s recent publication in BBA – Chin-Chi Chang; Md Imran  Khan; Kun-Lin Tsai; Hongchun Li; Lee-Wei Yang*; Ruey-Hwang Chou*; Chin Yu* (2016) Blocking the interaction between S100A9 and RAGE V domain using CHAPS molecule: A novel route to drug development against cell proliferation. BBA – Proteins and Proteomics [impact factor = 3.3]!  (Aug 2016)

Congratulations to Mr Yuan-Yu Chang who won the honorable mention (佳作) in oral presentation of published papers at 2016 NTHU&NCTU graduate students’ academic conference (2016 清交生科院研究生學術研討會)  (May 2016) !

Congratulations to Mr Emmanuel O Salawu’s and Mr Yuan-Yu Chang’s co-authored Scientific Reports paper got accepted!  Wen-Ting Chen, Wen-Yang Huang, Ting Wen, Emmanuel Oluwatobi Salawu, Dongli Wang, Yi-Zong Lee, Yuan-Yu Chang, Lee-Wei Yang, Shih-Che Sue, Xinquan Wang, and Hsien-Sheng Yin* (2016) Structure and function of chicken interleukin-1 beta mutants: uncoupling of receptor binding and in vivo biological activity. Scientific Reports [impact factor = 5.3] (May 2016) !

Congratulations to Mr Kai-Chun Chang who won the first prize of the poster competition in the 21st Biophysics Society Meeting in Taiwan (May 2016) !

Congratulations to Hongchun Li and Yuan-Yu Chang for the acceptance of their recent work published in NAR – Hongchun Li, Yuan-Yu Chang, Yang, L-W.* and Ivet Bahar* (2015) iGNM 2.0: The Gaussian Network Model Database for Biomolecular Structural Dynamics. Nucleic Acids Research, doi: 10.1093/nar/gkv1236 (Dec 2015) [impact factor = 9.1] !! (Dec 2015)

Congratulations to Mr Chris Yen-Chen Lo who was chosen and given scholarship to attend the Higher European Research Course for Users of Large Experimental Systems (HERCULES) 2016 Course from Tuesday March 29th to Friday April 29th, on session B including 6 days in Paris at SOLEIL Synchrotron or Laboratoire Léon Brillouin or in Switzerland at Swiss Light Source or in Hamburg at DESY or in Italy at Elettra in Trieste (Dec 2015) !!

Congratulations to Mr Yuan-Yu Chang became one of the three 2015 LS college Ph.D new student scholarship awardees (104學年度生科院博士班新生獎學金; 24,000NT/month) !!! (Oct 2015)


A new Review article from Kai-Chun Chang, Profs Wen and Yang was just published Kai-Chun Chang, Jin-Der Wen and Lee-Wei Yang (2015) Functional Importance of Mobile Ribosomal Proteins. BioMed Research International, V2015, Article ID 539238 (Sept 2015)

CONGRATULATIONS to Mr 張簡啟宏 who successfully defended his Master thesis. (July 2015) !!

Congratulations to Mr Yuan-Yu Chang for obatining a poster award (among Master student participants) in the 2015 College of Life Science Graduate Student Sympoisum, NTHU (2000NT cash prize)(June 2015)

Congratulations to Mr Mick Lin for obatining the undergraduate research fund provided by Ministry of Science and Technology (48K NT for a year); 恭喜 Mr 林泓叡之研究專題「發展以結構和動態為主的物理指標來預測分子演化的保守性」獲得104學年科技部獎勵大專生進行專題研究計畫獲補助  (May 2015)

CONGRATULATIONS to Mr 張芫瑜 who successfully defended his Master thesis and passed the PhD entrance exam of NTHU (結構生物學程). (May 2015)

Congratulations to Dr Bang-Chiech Huang obatining Poster Award in 第六屆海峽兩岸理論與計算化學(Theoretical and Computational Chemistry)會議壁報論文展 for the title “Intramolecular communications and allosteric regulations revealed by linear response theories”  (Jan 2015)

Congratulations to Dr Bang-Chiech Huang obatining MOST postdoc fellowship for a year (~1M a year); 恭喜 黃邦杰博士獲得「延攬科技人才及兩岸科技交流(延攬博士後研究人才)」補助一年  (Nov 2014)

Congratulations to Mr Kun-Lin Tsai obatining Scholarship of Shen’s Culture & Education Foundation (50K for 10 months); 恭喜 Mr 蔡坤霖獲得103學年度沈巨塵先生清華獎學金「優秀學生研究獎學金」  (Nov 2014)

Congratulations to Mr Mick Lin obatining the undergraduate research fund provided by Life Science College (30K for a year); 恭喜 Mr 林泓叡 之研究專題「藉由蛋白結構中原子間作用力觀察與演化上的比對建立結構與演化之間的關係」獲得103學年清華大學生命科學院獎勵大學生進行專題研究計畫獲補助; 獲獎人中唯一十六級的學生(其餘為十五級)  (Sept 2014)

CONGRATULATIONS to Dr Hongchun Li who just defended the thesis and obatined his PhD degree as well as accepted an offer from University of Pittsburgh, as a postdoctoral fellow, to continue his work on protein conformational dynamics and drug design. [[[狂賀!!!]]] 博班生李紅春獲得博士學位(28歲)並即將在十一月底前往匹茲堡大學醫學院進行博士後研究。(Sept 2014)

Ms Jia-Chen Wu accepted the offer of a RA position to study the energy basis for enantiomer selectivity and develop a theoretical platform to predict relevant enzymes’ specificity/selectivity for different substrates in Prof S.W. Tsai’s lab (Aug 2014)

New member was born !!!  Dr Ban-Chieh Huang’s third boy was born at 5:00 pm, 7/24, 2014.  Congratulations !!!  (July  2014)

New articles accepted  (July  2014)

Hongchun Li, Shun Sakuraba, Aravind Chandrasekaran and Lee-Wei Yang* (2014) Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs) J.Chem. Inf. Model. (IF: 4.3; Ranking: 3/100 in Computer Science)(accepted)

Lee W Yang, Akio Kitao, Bang-Chieh Huang and Nobuhiro Gō (2014) Ligand-induced Protein Responses and Mechanical Signal Propagation described by Linear Response Theories. Biophysical Journal, 107 (IF: 4.0)(accepted)

Mr Aravind Chandrasekaran decided to accept the offer provided by Dept of Chemistry in U Maryland to continue his academic pursue, as a PhD student,  in Computational Biology/Theretical Chemistry (Jun 2014)

Mr Aravind Chandrasekaran obtained admissions of PhD programs in University of Michigan at Ann Arbor, Baylor college of Medicine, University of Maryland and CMU-Pitt to continue his academic endeavors in Computational Biology/Chemistry (Mar 2014)

Ms Jia-Chen Wu successfully defended her Master thesis for her good work in the applicability of time-independent linear response theory for protein-ligand binding (Feb 2014)

Mr Aravind Chandrasekaran successfully defended his Master thesis for his good work on DNA – Protein interactions as a function of protein dynamics and contact topology (Feb 2014)

Mr Yen-Hua Chang successfully defended his Master thesis for his good work on predictions of enzyme active sites using partial least square regression over a set of sequence, structure and dynamics features (Oct 2013)

New article accepted  (Sept  2013)

Arun A. Gupta, Ruey-Hwang Chou, Hongchun Li, Lee-Wei Yang, Chin Yu, Structural Insights into the Interaction of Human S100B and Basic Fibroblast Growth Factor (FGF2): Effects on FGFR1 Receptor Signaling, BBA – Proteins and Proteomics (2013), doi: 10.1016/j.bbapap.2013.09.012

New article published  (May  2013)

Title: The N-terminal substrate-recognition domain of a LonC protease exhibits structural and functional similarity to cytosolic chaperones
Author(s):  Jhen-Kai Li,  Jiahn-Haur Liao,  Hongchun Li,  Chiao-I  Kuo,  Kai-Fa Huang,  Lee-Wei  Yang,  Shih-Hsiung  Wu and  Chung-I Chang*has been accepted for publication in Acta Crystallographica Section D (2013). D69, 1789–1797

New Editorial published  (Dec  2012)

Lee-Wei Yang, Silvina Matysiak, Shang-Te Danny Hsu, Gabriela Mustata Wilson, and Yasumasa Joti (2012) Functional Dynamics of Proteins. Computational and Mathemaical Methods in Medicine, 2012, 1-3

New article published  (Apr  2011)