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Lee-Wei Yang, Ph.D. - Publications

Affiliations: 
2005 University of Pittsburgh, Pittsburgh, PA, United States 
Area:
Medical Biophysics, Molecular Biology
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31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Banerjee A, Saha S, Tvedt NC, Yang LW, Bahar I. Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods. Current Opinion in Structural Biology. 78: 102517. PMID 36587424 DOI: 10.1016/j.sbi.2022.102517  0.559
2019 Huang BC, Yang LW. Molecular dynamics simulations and linear response theories jointly describe biphasic responses of myoglobin relaxation and reveal evolutionarily conserved frequent communicators. Biophysics and Physicobiology. 16: 473-484. PMID 31984199 DOI: 10.2142/Biophysico.16.0_473  0.359
2019 Chan J, Takemura K, Lin HR, Chang KC, Chang YY, Joti Y, Kitao A, Yang LW. An Efficient Timer and Sizer of Biomacromolecular Motions. Structure (London, England : 1993). PMID 31780433 DOI: 10.1016/J.Str.2019.10.020  0.382
2019 Chan J, Zou J, Ortiz CL, Chien CC, Pan RL, Yang LW. DR-SIP: Protocols for Higher Order Structure Modeling with Distance Restraints- and Cyclic Symmetry-Imposed Packing. Bioinformatics (Oxford, England). PMID 31347658 DOI: 10.1093/Bioinformatics/Btz579  0.379
2018 Chang KC, Salawu EO, Chang YY, Wen JD, Yang LW. Resolution-exchanged structural modeling and simulations jointly unravel that subunit rolling underlies the mechanism of programmed ribosomal frameshifting. Bioinformatics (Oxford, England). PMID 30169551 DOI: 10.1093/Bioinformatics/Bty762  0.363
2017 Li H, Chang YY, Lee JY, Bahar I, Yang LW. DynOmics: dynamics of structural proteome and beyond. Nucleic Acids Research. PMID 28472330 DOI: 10.1093/Nar/Gkx385  0.599
2016 Yin JC, Fei CH, Lo YC, Hsiao YY, Chang JC, Nix JC, Chang YY, Yang LW, Huang IH, Wang S. Structural Insights into Substrate Recognition by Clostridium difficile Sortase. Frontiers in Cellular and Infection Microbiology. 6: 160. PMID 27921010 DOI: 10.3389/Fcimb.2016.00160  0.35
2016 Chandrasekaran A, Chan J, Lim C, Yang LW. Protein dynamics and contact topology reveal protein-DNA binding orientation. Journal of Chemical Theory and Computation. PMID 27723319 DOI: 10.1021/Acs.Jctc.6B00688  0.414
2015 Li H, Chang YY, Yang LW, Bahar I. iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Research. PMID 26582920 DOI: 10.1093/Nar/Gkv1236  0.61
2015 Chang KC, Wen JD, Yang LW. Functional Importance of Mobile Ribosomal Proteins. Biomed Research International. 2015: 539238. PMID 26457300 DOI: 10.1155/2015/539238  0.388
2014 Yang LW, Kitao A, Huang BC, Gō N. Ligand-induced protein responses and mechanical signal propagation described by linear response theories. Biophysical Journal. 107: 1415-25. PMID 25229149 DOI: 10.1016/J.Bpj.2014.07.049  0.324
2014 Li H, Sakuraba S, Chandrasekaran A, Yang LW. Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs) Journal of Chemical Information and Modeling. 54: 2275-2285. PMID 25089914 DOI: 10.1021/Ci500261Z  0.442
2013 Li JK, Liao JH, Li H, Kuo CI, Huang KF, Yang LW, Wu SH, Chang CI. The N-terminal substrate-recognition domain of a LonC protease exhibits structural and functional similarity to cytosolic chaperones. Acta Crystallographica. Section D, Biological Crystallography. 69: 1789-97. PMID 23999302 DOI: 10.1107/S090744491301500X  0.32
2012 Yang LW, Matysiak S, Hsu ST, Mustata Wilson G, Joti Y. Functional dynamics of proteins. Computational and Mathematical Methods in Medicine. 2012: 242903. PMID 23346219 DOI: 10.1155/2012/242903  0.447
2012 Chang K, Wen J, Yang L. Modelling Programmed Ribosomal Frameshifting with Elastic Network Model and Linear Response Theory Biophysical Journal. 102: 70a. DOI: 10.1016/J.Bpj.2011.11.407  0.361
2010 Bahar I, Lezon TR, Yang LW, Eyal E. Global dynamics of proteins: bridging between structure and function. Annual Review of Biophysics. 39: 23-42. PMID 20192781 DOI: 10.1146/Annurev.Biophys.093008.131258  0.613
2009 Yang LW, Eyal E, Bahar I, Kitao A. Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinformatics (Oxford, England). 25: 606-14. PMID 19147661 DOI: 10.1093/Bioinformatics/Btp023  0.551
2008 Chng CP, Yang LW. Coarse-grained models reveal functional dynamics--II. Molecular dynamics simulation at the coarse-grained level--theories and biological applications. Bioinformatics and Biology Insights. 2: 171-85. PMID 19812774 DOI: 10.4137/Bbi.S459  0.407
2008 Yang LW, Chng CP. Coarse-grained models reveal functional dynamics--I. Elastic network models--theories, comparisons and perspectives. Bioinformatics and Biology Insights. 2: 25-45. PMID 19812764 DOI: 10.4137/Bbi.S460  0.408
2007 Eyal E, Chennubhotla C, Yang LW, Bahar I. Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. Bioinformatics (Oxford, England). 23: i175-84. PMID 17646294 DOI: 10.1093/bioinformatics/btm186  0.489
2007 Yang LW, Eyal E, Chennubhotla C, Jee J, Gronenborn AM, Bahar I. Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-Ray Data with Computational Predictions Structure. 15: 741-749. PMID 17562320 DOI: 10.1016/J.Str.2007.04.014  0.515
2007 Yang L, Nishima W, Kitao A. 2P013 Dynomics portal : An integral effort on developing and organizing dynamics web servers/databases(Proteins-structure and structure-function relationship,Oral Presentations) Seibutsu Butsuri. 47: S116. DOI: 10.2142/Biophys.47.S116_2  0.382
2006 Eyal E, Yang LW, Bahar I. Anisotropic network model: systematic evaluation and a new web interface. Bioinformatics (Oxford, England). 22: 2619-27. PMID 16928735 DOI: 10.1093/Bioinformatics/Btl448  0.537
2006 Yang LW, Rader AJ, Liu X, Jursa CJ, Chen SC, Karimi HA, Bahar I. oGNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Research. 34: W24-31. PMID 16845002 DOI: 10.1093/Nar/Gkl084  0.6
2005 Berberich JA, Yang LW, Bahar I, Russell AJ. A stable three enzyme creatinine biosensor. 2. Analysis of the impact of silver ions on creatine amidinohydrolase. Acta Biomaterialia. 1: 183-91. PMID 16701795 DOI: 10.1016/J.Actbio.2004.11.007  0.439
2005 Berberich JA, Yang LW, Madura J, Bahar I, Russell AJ. A stable three-enzyme creatinine biosensor. 1. Impact of structure, function and environment on PEGylated and immobilized sarcosine oxidase. Acta Biomaterialia. 1: 173-81. PMID 16701794 DOI: 10.1016/J.Actbio.2004.11.006  0.422
2005 Chennubhotla C, Rader AJ, Yang LW, Bahar I. Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies. Physical Biology. 2: S173-80. PMID 16280623 DOI: 10.1088/1478-3975/2/4/S12  0.623
2005 Yang LW, Bahar I. Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure (London, England : 1993). 13: 893-904. PMID 15939021 DOI: 10.1016/J.Str.2005.03.015  0.541
2005 Yang LW, Liu X, Jursa CJ, Holliman M, Rader AJ, Karimi HA, Bahar I. iGNM: a database of protein functional motions based on Gaussian Network Model. Bioinformatics (Oxford, England). 21: 2978-87. PMID 15860562 DOI: 10.1093/Bioinformatics/Bti469  0.604
2004 Seki M, Masutani C, Yang LW, Schuffert A, Iwai S, Bahar I, Wood RD. High-efficiency bypass of DNA damage by human DNA polymerase Q. The Embo Journal. 23: 4484-94. PMID 15496986 DOI: 10.1038/Sj.Emboj.7600424  0.397
2004 Liu X, Karimi HA, Yang LW, Bahar I. Protein functional motion query and visualization Proceedings - International Computer Software and Applications Conference. 2: 86-89. DOI: 10.1109/CMPSAC.2004.1342683  0.554
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