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Homology Modeling of Human Serine Racemase and Its Molecular Docking with Peptide Inhibitors

ZHAO Yong-Shan, 吉林大学理论化学研究所, 理论化学计算国家重点实验室, 长春 130023, State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China
2009 Wuli huaxue xuebao  
Fig. 5 5 Main鄄chaindihedralangles(Ramachandran plot)ofthemodeledhumanserineracemase A,B,andLrepresenttheresiduesinmostfavouredregions;a,b,l, andprepresenttheresiduesinadditionalallowedregions;~a,~b,~l, and  ...  所有量子化学计算 由 Gaussian03 程序包 [26] 来完成的. 2 结果与讨论 2.1 hSR 三维结构的同源模建 由自动模建程序 modeler 构建的初始模型, 经 图 1 多肽类抑制剂 A 和 B 的结构示意图 Fig.1 StructuresofpeptideinhibitorsAandB No.3 赵勇山等:人类丝氨酸消旋酶的同源模建及其与多肽类抑制剂的分子对接 过能量最小化和分子动力学模拟后  ... 
doi:10.3866/pku.whxb20090304 fatcat:yoyc32s2tffgjk3u3rmrj5iyjy

The Universal Plausibility Metric (UPM) & Principle (UPP)

David L Abel
2009 Theoretical Biology and Medical Modelling  
A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified.  ...  Both UPM and UPP pre-exist and are independent of any experimental design and data set.  ...  Philosophic and especially religious perspectives have no place in scientific literature, and are irrelevant to the technical UPM calculation and UPP presented in this paper.  ... 
doi:10.1186/1742-4682-6-27 pmid:19958539 pmcid:PMC2796651 fatcat:hzura2lvtvd7fcbzguky7hfy6q

Computer-Aided Design of Antimicrobial Peptides

Christopher D. Fjell, Robert E.W. Hancock, Havard Jenssen
2010 Current Pharmaceutical Analysis  
(PCA) and a non-linear artificial neural network model.  ...  In this review we will discuss two different in silico strategies of computer-aided antibacterial peptide design, a linear correlation model build as an extension of traditional principal component analysis  ...  ACKNOWLEDGEMENT We gratefully acknowledge financial support through grants from the Canadian Institutes for Health Research (CIHR) and the Applied Food and Materials Network.  ... 
doi:10.2174/157341210791202645 fatcat:6ditllvydjbvpbymjeuxmvjdg4

Peptides as versatile scaffolds for quantum computing [article]

Lorena E. Rosaleny, Alicia Forment-Aliaga, Helena Prima-García, Ramón Torres Cavanillas, José J. Baldoví, Violetta Gołȩbiewska, Karolina Wlazło, Garin Escorcia-Ariza, Luis Escalera-Moreno, Sergio Tatay, Carolina García-Llácer, Miguel Clemente-León, Salvador Cardona-Serra, Patricia Casino, Luis Martínez-Gil, Alejandro Gaita-Ariño (+1 others)
2017 arXiv   pre-print
In this work we showcase the potential of peptides as versatile scaffolds for quantum computing and molecular spintronics.  ...  Finally, we take advantage of biochemical modification for the preparation of paramagnetic, chiral, Self-Assembled Monolayers (SAMs) on Au(111).Our experimental and theoretical characterization shows that  ...  To calculate the theoretical coverage of the surface two different models have been used that give rise to a range of coverage values: -Model A: the molecule is considered as a cube of 1.7 nm side -Model  ... 
arXiv:1708.09440v2 fatcat:sho6kwckafdipeftm6m6w2o55e

Software for computational peptide identification from MS–MS data

Changjiang Xu, Bin Ma
2006 Drug Discovery Today  
Computational methods are then invoked to identify the peptides, which are later combined together to identify the protein.  ...  Because of the difficulty of measuring intact proteins using MS-MS, typically a protein is enzymically digested into peptides and the MS-MS spectrum of each peptide is measured.  ...  The theoretical spectrum of the peptide sequence is computed using a simple model. The spectrum is then displaced by adding a displacement value t to the m/z value of each peak.  ... 
doi:10.1016/j.drudis.2006.05.011 pmid:16793527 fatcat:unyquazdp5dzfah2omkfq7qoq4

Computational Design of Peptide Ligands for Ochratoxin A

Meike Heurich, Zeynep Altintas, Ibtisam Tothill
2013 Toxins  
In this paper, we describe a peptide library designed by computational modelling and the selection of two peptide sequences showing affinity towards the mycotoxin, ochratoxin A (OTA).  ...  This work illustrates the potential of using computational modelling to design a peptide sequence that exhibits in vitro binding affinity for a small molecular weight toxin.  ...  Here, we present the application of computational modelling for a peptide ligand designed for ochratoxin A binding.  ... 
doi:10.3390/toxins5061202 pmid:23793075 pmcid:PMC3717777 fatcat:k22bgt56kvcbbdw6nletgydeoq

Computational prediction of proteotypic peptides for quantitative proteomics

Parag Mallick, Markus Schirle, Sharon S Chen, Mark R Flory, Hookeun Lee, Daniel Martin, Jeffrey Ranish, Brian Raught, Robert Schmitt, Thilo Werner, Bernhard Kuster, Ruedi Aebersold
2006 Nature Biotechnology  
Characteristic physicochemical properties of these peptides were used to develop a computational tool that can predict proteotypic peptides for any protein from any organism, for a given platform, with  ...  Although such analyses typically assume that a protein's peptide fragments are observed with equal likelihood, only a few so-called 'proteotypic' peptides are repeatedly and consistently identified for  ...  ACKNOWLEDGMENTS The authors are grateful to Julien Gagneur for fruitful discussions and the Cellzome biochemistry, mass spectrometry and informatics teams for generating and managing data.  ... 
doi:10.1038/nbt1275 pmid:17195840 fatcat:aqfp3cpsqfggrmvnbmqua6zwk4

Toward computational determination of peptide-receptor structure

Ugur Sezerman, Sandor Vajda, James Cornette, Charles Delisi
1993 Protein Science  
After developing the method we apply it to peptide-MHC class I systems and find that the predictions are in accord with biological and crystallographic data.  ...  We introduce a method for docking small flexible ligands of the size of dipeptides and phosphocholine and test it against crystallographic complexes.  ...  expected theoretically (DeLisi & Berzofsky, 1985) .  ... 
doi:10.1002/pro.5560021105 pmid:7505681 pmcid:PMC2142284 fatcat:pznshg6ufzddrp5qtrohhtxlqy

New computational approaches for de novo peptide sequencing from MS/MS experiments

O. Lubeck, C. Sewell, Sheng Gu, Xian Chen, D.M. Cai
2002 Proceedings of the IEEE  
These new approaches integrate chemical information and knowledge into a graph-theoretic framework.  ...  We describe computational methods to solve the problem of identifying novel proteins from tandem mass spectrometry (tandem MS or MS/MS) data and introduce new approaches that will give more accurate solutions  ...  Most recently, a group at Harvard Medical Center has reported on a dynamic programming approach [7] ; a pharmaceutical and university consortium have shown some progress with graph-theoretical approaches  ... 
doi:10.1109/jproc.2002.805301 fatcat:bbhkcmjvarda7f4txtr757cxky

Activity Determinants of Helical Antimicrobial Peptides: A Large-Scale Computational Study

Yi He, Themis Lazaridis, Spencer J. Williams
2013 PLoS ONE  
Here we test this hypothesis by using binding free energy data collected from the literature and theoretical binding energies calculated from implicit membrane models for 53 helical AMPs.  ...  The majority of these peptides are cationic and are thought to function by permeabilizing the bacterial membrane, either by making pores or by dissolving it ('carpet' model).  ...  These are obtained here theoretically using an implicit membrane model.  ... 
doi:10.1371/journal.pone.0066440 pmid:23776672 pmcid:PMC3680375 fatcat:dpfg5lg5cjafllv6uzzegitrhe

Solving peptide sequencing as satisfiability

Renato Bruni
2008 Computers and Mathematics with Applications  
Data obtained from the mass spectrometry analysis of a peptide are used to build a propositional logic formula, whose models represent coherent interpretations of that set of data and can be used to generate  ...  Some computational results on real-world peptide analysis problems are reported, which show the effectiveness of our approach.  ...  Gigi Gianfranceschi, from the University of Perugia, and to Prof.  ... 
doi:10.1016/j.camwa.2006.12.094 fatcat:5bjokda3y5aepgiqdg5nzhkwj4

Vibrational circular dichroism of tetraphenylporphyrin in peptide complexes? A computational study

Petr Bou?, Kamil Z�ruba, Marie Urbanov�, Vladim�r Setni?ka, Pavel Mat?jka, Zden?k Fiedler, Vladim�r Kr�l, Karel Volka
2000 Chirality  
Such spectra were compared to theoretical VCD intensities of a model tripeptide as well to experimental spectra of a complex of the peptide and tetrakis(p-sulfonatophenyl)porphyrin (TSPP).  ...  The computation was based on the harmonic molecular force field and electric tensors obtained ab initio at the BPW91/6-31G* level.  ...  ACKNOWLEDGMENT Computations were performed at the Supercomputer Center in Prague and at computer facilities of the University of Illinois at Chicago.  ... 
doi:10.1002/(sici)1520-636x(2000)12:4<191::aid-chir5>3.0.co;2-w pmid:10790189 fatcat:w2por6yykrdcxaehi37tgcyk2i

On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective

Konda Mani Saravanan, Haiping Zhang, Huiling Zhang, Wenhui Xi, Yanjie Wei
2020 Frontiers in Bioengineering and Biotechnology  
Many theoretical models have been proposed in the recent years for studying Aβ peptides using mathematical, physicochemical, and molecular dynamics simulation, and machine learning approaches.  ...  In this article, we have comprehensively reviewed the developmental advances in the theoretical models for Aβ peptide folding and interactions, particularly in the context of neurological disorders.  ...  AUTHOR CONTRIBUTIONS KS, HaZ, and HuZ are the co-first authors who drafted the manuscript. WX and YW are corresponding authors who supervised and revised the draft.  ... 
doi:10.3389/fbioe.2020.00532 pmid:32656188 pmcid:PMC7325929 fatcat:puuzhk7r4zfhnnm5hieki7bdju

Computer determination of peptide conformations in water: different roads to structure

C. L. Simmerling, R. Elber
1995 Proceedings of the National Academy of Sciences of the United States of America  
We used a computational method to determine structures of two foldable peptides in explicit water: RVEW and CSVTC.  ...  The optimization starts from random structures and no experimental constraints are used. In agreement with NMR data, the simulations find a hydrophobic pair (Val/Trp) in RVEW.  ...  Chaim Gilon for his suggestion to study the peptide CSVTC. This research was supported by National Institutes of Health Grant GM41905. R.E. is an Alon fellow in the Hebrew University."  ... 
doi:10.1073/pnas.92.8.3190 pmid:7724538 pmcid:PMC42131 fatcat:2rd6ks6nabetdf7wmn7cc3rgi4

The computer modelling of human TRH receptor, TRH and TRH-like peptides

R Bílek, L Stárka
2005 Physiological Research  
Gasteiger, Computer-Chemie-Centrum and Institute for Organic Chemistry, University of Erlangen-Nurenberg, Germany).  ...  . 3D-structures of TRH-like peptides were determined with a computer program CORINA (written by the team of J.  ...  The work was supported by the grant No. 6712-3, 6778-4 of the Internal Grant Agency and by the grant No MZ:000000023761.  ... 
pmid:15544424 fatcat:diiajhzfnrgttkb6i5bctyqili
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