Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta (English)
- New search for: Ovchinnikov, Sergey
- New search for: Kim, David E.
- New search for: Wang, Ray Yu‐Ruei
- New search for: Liu, Yuan
- New search for: DiMaio, Frank
- New search for: Baker, David
- New search for: Ovchinnikov, Sergey
- New search for: Kim, David E.
- New search for: Wang, Ray Yu‐Ruei
- New search for: Liu, Yuan
- New search for: DiMaio, Frank
- New search for: Baker, David
In:
Proteins: Structure, Function, and Bioinformatics
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84
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67-75
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2016
- Article (Journal) / Electronic Resource
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Title:Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta
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Contributors:Ovchinnikov, Sergey ( author ) / Kim, David E. ( author ) / Wang, Ray Yu‐Ruei ( author ) / Liu, Yuan ( author ) / DiMaio, Frank ( author ) / Baker, David ( author )
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Published in:Proteins: Structure, Function, and Bioinformatics ; 84 ; 67-75
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Publisher:
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Publication date:2016-09-01
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Size:9 pages
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ISSN:
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DOI:
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Type of media:Article (Journal)
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Type of material:Electronic Resource
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Language:English
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Keywords:
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Source:
Table of contents – Volume 84
The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.
- 1
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Issue Information ‐ Table of Content| 2016
- 3
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Predicting protein folding rate change upon point mutation using residue‐level coevolutionary informationMallik, Saurav / Das, Smita / Kundu, Sudip et al. | 2016
- 4
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Critical assessment of methods of protein structure prediction: Progress and new directions in round XIMoult, John / Fidelis, Krzysztof / Kryshtafovych, Andriy / Schwede, Torsten / Tramontano, Anna et al. | 2016
- 9
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High‐resolution crystal structures leverage protein binding affinity predictionsMarillet, Simon / Boudinot, Pierre / Cazals, Frédéric et al. | 2016
- 15
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CASP11 statistics and the prediction center evaluation systemKryshtafovych, Andriy / Monastyrskyy, Bohdan / Fidelis, Krzysztof et al. | 2016
- 20
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CASP 11 target classificationKinch, Lisa N. / Li, Wenlin / Schaeffer, R. Dustin / Dunbrack, Roland L. / Monastyrskyy, Bohdan / Kryshtafovych, Andriy / Grishin, Nick V. et al. | 2016
- 21
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Archeal lectins: An identification through a genomic searchAbhinav, K. V. / Samuel, Ebenezer / Vijayan, M. et al. | 2016
- 31
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Anabaena sp. DyP‐type peroxidase is a tetramer consisting of two asymmetric dimersYoshida, Toru / Ogola, Henry Joseph Oduor / Amano, Yoshimi / Hisabori, Toru / Ashida, Hiroyuki / Sawa, Yoshihiro / Tsuge, Hideaki / Sugano, Yasushi et al. | 2016
- 34
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Some of the most interesting CASP11 targets through the eyes of their authorsKryshtafovych, Andriy / Moult, John / Baslé, Arnaud / Burgin, Alex / Craig, Timothy K. / Edwards, Robert A. / Fass, Deborah / Hartmann, Marcus D. / Korycinski, Mateusz / Lewis, Richard J. et al. | 2016
- 43
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Interaction between bound water molecules and local protein structures: A statistical analysis of the hydrogen bond structures around bound water moleculesHong, Seungpyo / Kim, Dongsup et al. | 2016
- 51
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Evaluation of free modeling targets in CASP11 and ROLLKinch, Lisa N. / Li, Wenlin / Monastyrskyy, Bohdan / Kryshtafovych, Andriy / Grishin, Nick V. et al. | 2016
- 52
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Conformational fluctuations of the AXH monomer of Ataxin‐1Grasso, Gianvito / Deriu, Marco A. / Tuszynski, Jack A. / Gallo, Diego / Morbiducci, Umberto / Danani, Andrea et al. | 2016
- 60
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Toward rational thermostabilization of Aspergillus oryzae cutinase: Insights into catalytic and structural stabilityShirke, Abhijit N. / Basore, Danielle / Butterfoss, Glenn L. / Bonneau, Richard / Bystroff, Christopher / Gross, Richard A. et al. | 2016
- 67
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Improved de novo structure prediction in CASP11 by incorporating coevolution information into RosettaOvchinnikov, Sergey / Kim, David E. / Wang, Ray Yu‐Ruei / Liu, Yuan / DiMaio, Frank / Baker, David et al. | 2016
- 73
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Molecular dynamics of water and monovalent‐ions transportation mechanisms of pentameric sarcolipinCao, Yipeng / Wu, Xue / Lee, Imshik / Wang, Xinyu et al. | 2016
- 76
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Integration of QUARK and I‐TASSER for Ab Initio Protein Structure Prediction in CASP11Zhang, Wenxuan / Yang, Jianyi / He, Baoji / Walker, Sara Elizabeth / Zhang, Hongjiu / Govindarajoo, Brandon / Virtanen, Jouko / Xue, Zhidong / Shen, Hong‐Bin / Zhang, Yang et al. | 2016
- 82
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Visualizing global properties of a molecular dynamics trajectoryZhou, Hao / Li, Shangyang / Makowski, Lee et al. | 2016
- 87
-
Analysis of free modeling predictions by RBO aleph in CASP11Mabrouk, Mahmoud / Werner, Tim / Schneider, Michael / Putz, Ines / Brock, Oliver et al. | 2016
- 92
-
Refining the treatment of membrane proteins by coarse‐grained modelsVorobyov, Igor / Kim, Ilsoo / Chu, Zhen T. / Warshel, Arieh et al. | 2016
- 105
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Protein structure prediction using residue‐ and fragment‐environment potentials in CASP11Kim, Hyungrae / Kihara, Daisuke et al. | 2016
- 118
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Structure and functional analysis of the siderophore periplasmic binding protein from the fuscachelin gene cluster of Thermobifida fuscaLi, Kunhua / Bruner, Steven D. et al. | 2016
- 118
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Template‐free modeling by LEE and LEER in CASP11Joung, InSuk / Lee, Sun Young / Cheng, Qianyi / Kim, Jong Yun / Joo, Keehyoung / Lee, Sung Jong / Lee, Jooyoung et al. | 2016
- 129
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Probing the roles of two tryptophans surrounding the unique zinc coordination site in lipase family I.5Timucin, Emel / Cousido‐Siah, Alexandra / Mitschler, André / Podjarny, Alberto / Sezerman, Osman Ugur et al. | 2016
- 131
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New encouraging developments in contact prediction: Assessment of the CASP11 resultsMonastyrskyy, Bohdan / D'Andrea, Daniel / Fidelis, Krzysztof / Tramontano, Anna / Kryshtafovych, Andriy et al. | 2016
- 143
-
Stability strengths and weaknesses in protein structures detected by statistical potentials: Application to bovine seminal ribonucleaseDe Laet, Marie / Gilis, Dimitri / Rooman, Marianne et al. | 2016
- 145
-
Accurate contact predictions using covariation techniques and machine learningKosciolek, Tomasz / Jones, David T. et al. | 2016
- 152
-
Blind testing of cross‐linking/mass spectrometry hybrid methods in CASP11Schneider, Michael / Belsom, Adam / Rappsilber, Juri / Brock, Oliver et al. | 2016
- 159
-
Molecular dynamics simulations elucidate the mode of protein recognition by Skp1 and the F‐box domain in the SCF complexChandra Dantu, Sarath / Nathubhai Kachariya, Nitin / Kumar, Ashutosh et al. | 2016
- 164
-
Assessment of CASP11 contact‐assisted predictionsKinch, Lisa N. / Li, Wenlin / Monastyrskyy, Bohdan / Kryshtafovych, Andriy / Grishin, Nick V. et al. | 2016
- 172
-
A composite approach towards a complete model of the myosin rodKorkmaz, E. Nihal / Taylor, Keenan C. / Andreas, Michael P. / Ajay, Guatam / Heinze, Nathan T. / Cui, Qiang / Rayment, Ivan et al. | 2016
- 181
-
Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11Ovchinnikov, Sergey / Park, Hahnbeom / Kim, David E. / Liu, Yuan / Wang, Ray Yu‐Ruei / Baker, David et al. | 2016
- 189
-
Contact‐assisted protein structure modeling by global optimization in CASP11Joo, Keehyoung / Joung, InSuk / Cheng, Qianyi / Lee, Sung Jong / Lee, Jooyoung et al. | 2016
- 193
-
Mycobacterium tuberculosis copper‐regulated protein SocB is an intrinsically disordered protein that folds upon interaction with a synthetic phospholipid bilayerNowicka, Urszula et al. | 2016
- 200
-
Assessment of template‐based modeling of protein structure in CASP11Modi, Vivek / Xu, Qifang / Adhikari, Sam / Dunbrack, Roland L. Jr. et al. | 2016
- 201
-
An amino acid code to define a protein's tertiary packing surfaceJoo, Hyun et al. | 2016
- 217
-
Fast assessment of structural models of ion channels based on their predicted current–voltage characteristicsDyrka, Witold et al. | 2016
- 221
-
Template based protein structure modeling by global optimization in CASP11Joo, Keehyoung / Joung, InSuk / Lee, Sun Young / Kim, Jong Yun / Cheng, Qianyi / Manavalan, Balachandran / Joung, Jong Young / Heo, Seungryong / Lee, Juyong / Nam, Mikyung et al. | 2016
- 232
-
Investigating the linkage between disease‐causing amino acid variants and their effect on protein stability and bindingPeng, Yunhui et al. | 2016
- 233
-
Template‐based protein structure prediction in CASP11 and retrospect of I‐TASSER in the last decadeYang, Jianyi / Zhang, Wenxuan / He, Baoji / Walker, Sara Elizabeth / Zhang, Hongjiu / Govindarajoo, Brandon / Virtanen, Jouko / Xue, Zhidong / Shen, Hong‐Bin / Zhang, Yang et al. | 2016
- 240
-
Redesigning the stereospecificity of tyrosyl‐tRNA synthetaseYe‐Lehmann, Shixin et al. | 2016
- 247
-
Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11Cao, Renzhi / Bhattacharya, Debswapna / Adhikari, Badri / Li, Jilong / Cheng, Jianlin et al. | 2016
- 254
-
Wetting of nonconserved residue‐backbones: A feature indicative of aggregation associated regions of proteinsVerma, Chandra S et al. | 2016
- 260
-
Assessment of refinement of template‐based models in CASP11Modi, Vivek / Dunbrack, Roland L. Jr. et al. | 2016
- 267
-
Dynamics and allostery of the ionotropic glutamate receptors and the ligand binding domainTobi, Dror et al. | 2016
- 278
-
Cy‐preds: An algorithm and a web service for the analysis and prediction of cysteine reactivitySoylu, İnanç et al. | 2016
- 282
-
Protein structure refinement via molecular‐dynamics simulations: What works and what does not?Feig, Michael / Mirjalili, Vahid et al. | 2016
- 408
-
Issue Information ‐ Forthcoming| 2016
- 293
-
Effective protein model structure refinement by loop modeling and overall relaxationLee, Gyu Rie / Heo, Lim / Seok, Chaok et al. | 2016
- 295
-
Strategies to reduce end‐product inhibition in family 48 glycoside hydrolasesChen, Mo / Bu, Lintao / Alahuhta, Markus / Brunecky, Roman / Xu, Qi / Lunin, Vladimir V. / Brady, John W. / Crowley, Michael F. / Himmel, Michael E. / Bomble, Yannick J. et al. | 2016
- 302
-
Protein structure refinement with adaptively restrained homologous replicasDella Corte, Dennis / Wildberg, André / Schröder, Gunnar F. et al. | 2016
- 305
-
Water and ion permeability of a claudin model: A computational studyLaghaei, Rozita / Yu, Alan S. L. / Coalson, Rob D. et al. | 2016
- 314
-
CASP11 refinement experiments with ROSETTAPark, Hahnbeom / DiMaio, Frank / Baker, David et al. | 2016
- 316
-
Structure and functional characterization of a bile acid 7[alpha] dehydratase BaiE in secondary bile acid synthesisShiva Bhowmik et al. | 2016
- 316
-
Structure and functional characterization of a bile acid 7α dehydratase BaiE in secondary bile acid synthesisBhowmik, Shiva / Chiu, Hsien‐Po / Jones, David H. / Chiu, Hsiu‐Ju / Miller, Mitchell D. / Xu, Qingping / Farr, Carol L. / Ridlon, Jason M. / Wells, James E. / Elsliger, Marc‐André et al. | 2016
- 323
-
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experimentLensink, Marc F. / Velankar, Sameer / Kryshtafovych, Andriy / Huang, Shen‐You / Schneidman‐Duhovny, Dina / Sali, Andrej / Segura, Joan / Fernandez‐Fuentes, Narcis / Viswanath, Shruthi / Elber, Ron et al. | 2016
- 332
-
COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programmingZhang, Huiling / Huang, Qingsheng / Bei, Zhendong / Wei, Yanjie / Floudas, Christodoulos A. et al. | 2016
- 349
-
Methods of model accuracy estimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11Kryshtafovych, Andriy / Barbato, Alessandro / Monastyrskyy, Bohdan / Fidelis, Krzysztof / Schwede, Torsten / Tramontano, Anna et al. | 2016
- 349
-
Conformation of membrane‐bound proteins revealed by vacuum‐ultraviolet circular‐dichroism and linear‐dichroism spectroscopyMatsuo, Koichi / Maki, Yasuyuki / Namatame, Hirofumi / Taniguchi, Masaki / Gekko, Kunihiko et al. | 2016
- 360
-
New insight into the architecture of oxy‐anion pocket in unliganded conformation of GAT domains: A MD‐simulation studyBairagya, Hridoy R. / Bansal, Manju et al. | 2016
- 370
-
Biological function derived from predicted structures in CASP11Huwe, Peter J. / Xu, Qifang / Shapovalov, Maxim V. / Modi, Vivek / Andrake, Mark D. / Dunbrack, Roland L. Jr. et al. | 2016
- 374
-
Crystal structure of archaeal ketopantoate reductase complexed with coenzyme a and 2‐oxopantoate provides structural insights into feedback regulationAikawa, Yoshiki / Nishitani, Yuichi / Tomita, Hiroya / Atomi, Haruyuki / Miki, Kunio et al. | 2016
- 383
-
Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculationsCapoferri, Luigi / Leth, Rasmus / ter Haar, Ernst / Mohanty, Arun K. / Grootenhuis, Peter D. J. / Vottero, Eduardo / Commandeur, Jan N. M. / Vermeulen, Nico P. E. / Jørgensen, Flemming Steen / Olsen, Lars et al. | 2016
- 397
-
Identification of family determining residues in Jumonji‐C lysine demethylases: A sequence‐based, family wide classificationSlama, Patrick et al. | 2016
- 411
-
Toward a detailed understanding of search trajectories in fragment assembly approaches to protein structure predictionKandathil, Shaun M. / Handl, Julia / Lovell, Simon C. et al. | 2016
- 427
-
Epitope mapping and structural basis for the recognition of phosphorylated tau by the anti‐tau antibody AT8Malia, Thomas J. / Teplyakov, Alexey / Ernst, Robin / Wu, Sheng‐Jiun / Lacy, Eilyn R. / Liu, Xuesong / Vandermeeren, Marc / Mercken, Marc / Luo, Jinquan / Sweet, Raymond W. et al. | 2016
- 435
-
The role of negative selection in protein evolution revealed through the energetics of the native state ensembleHoffmann, Jordan / Wrabl, James O. / Hilser, Vincent J. et al. | 2016
- 448
-
A genetic and physical study of the interdomain linker of E. Coli AraC protein‐a trans‐subunit communication pathwayMalaga, Fabiana / Mayberry, Ory / Park, David J. / Rodgers, Michael E. / Toptygin, Dmitri / Schleif, Robert F. et al. | 2016
- 461
-
Solution structure of the calmodulin‐like C‐terminal domain of Entamoeba α‐actinin2Karlsson, Göran / Persson, Cecilia / Mayzel, Maxim / Hedenström, Mattias / Backman, Lars et al. | 2016
- 467
-
Protein‐fold recognition using an improved single‐source K diverse shortest paths algorithmLhota, John / Xie, Lei et al. | 2016
- 473
-
Exploring the unbinding of Leishmania (L.) amazonensis CPB derived‐epitopes from H2 MHC class I proteinsBrandt, Artur M. L. / Batista, Paulo Ricardo / Souza‐Silva, Franklin / Alves, Carlos Roberto / Caffarena, Ernesto Raul et al. | 2016
- 488
-
A2T and A2V Aβ peptides exhibit different aggregation kinetics, primary nucleation, morphology, structure, and LTP inhibitionMurray, Brian / Sorci, Mirco / Rosenthal, Joseph / Lippens, Jennifer / Isaacson, David / Das, Payel / Fabris, Daniele / Li, Shaomin / Belfort, Georges et al. | 2016
- 488
-
A2T and A2V A[beta] peptides exhibit different aggregation kinetics, primary nucleation, morphology, structure, and LTP inhibitionBrian Murray et al. | 2016
- 501
-
General trends of dihedral conformational transitions in a globular proteinMiao, Yinglong / Baudry, Jerome / Smith, Jeremy C. / McCammon, J. Andrew et al. | 2016
- 515
-
Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizesFerreira, Diogo C. / van der Linden, Marx G. / de Oliveira, Leandro C. / Onuchic, José N. / Pereira de Araújo, Antônio F. et al. | 2016
- 532
-
Computational analysis of the CB1 carboxyl‐terminus in the receptor‐G protein complexShim, Joong‐Youn / Khurana, Leepakshi / Kendall, Debra A. et al. | 2016
- 544
-
Ensemble models of proteins and protein domains based on distance distribution restraintsJeschke, Gunnar et al. | 2016
- 565
-
Spatial proximity statistics suggest a regulatory role of protein phosphorylation on compound bindingKorkuć, Paula / Walther, Dirk et al. | 2016
- 580
-
Model for the allosteric regulation of the Na+/Ca2+ exchanger NCXAbiko, Layara Akemi / Vitale, Phelipe M. / Favaro, Denize C. / Hauk, Pricila / Li, Da‐Wei / Yuan, Jiaqi / Bruschweiler‐Li, Lei / Salinas, Roberto K. / Brüschweiler, Rafael et al. | 2016
- 591
-
Structure of iron saturated C‐lobe of bovine lactoferrin at pH 6.8 indicates a weakening of iron coordinationRastogi, Nilisha / Singh, Avinash / Singh, Prashant K. / Tyagi, Tapesh K. / Pandey, Sada / Shin, Kouichirou / Kaur, Punit / Sharma, Sujata / Singh, Tej P. et al. | 2016
- 600
-
Identification of imine reductase‐specific sequence motifsFademrecht, Silvia / Scheller, Philipp N. / Nestl, Bettina M. / Hauer, Bernhard / Pleiss, Jürgen et al. | 2016
- 611
-
A hidden aggregation‐prone structure in the heart of hypoxia inducible factor prolyl hydroxylaseHadi‐Alijanvand, Hamid / Proctor, Elizabeth A. / Ding, Feng / Dokholyan, Nikolay V. / Moosavi‐Movahedi, Ali A. et al. | 2016
- 624
-
The respective roles of polar/nonpolar binary patterns and amino acid composition in protein regular secondary structures explored exhaustively using hydrophobic cluster analysisRebehmed, Joseph / Quintus, Flavien / Mornon, Jean‐Paul / Callebaut, Isabelle et al. | 2016
- 639
-
Unraveling the mechanism of proton translocation in the extracellular half‐channel of bacteriorhodopsinGe, Xiaoxia / Gunner, M. R. et al. | 2016
- 655
-
Function changing mutations in glucocorticoid receptor evolution correlate with their relevance to mode couplingKav, Batuhan / Öztürk, Murat / Kabakçιoğlu, Alkan et al. | 2016
- 666
-
Characterization of the AXH domain of Ataxin‐1 using enhanced sampling and functional mode analysisDeriu, Marco A. / Grasso, Gianvito / Tuszynski, Jack A. / Massai, Diana / Gallo, Diego / Morbiducci, Umberto / Danani, Andrea et al. | 2016
- 674
-
Mechanism and rate constants of the Cdc42 GTPase binding with intrinsically disordered effectorsPang, Xiaodong / Zhou, Huan‐Xiang et al. | 2016
- 686
-
The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculationsVícha, Jan / Babinský, Martin / Demo, Gabriel / Otrusinová, Olga / Jansen, Séverine / Pekárová, Blanka / Žídek, Lukáš / Munzarová, Markéta L. et al. | 2016
- 700
-
Introducing folding stability into the score function for computational design of RNA‐binding peptides boosts the probability of successXiao, Xingqing / Agris, Paul F. / Hall, Carol K. et al. | 2016
- 712
-
Crystal structure of translation initiation factor 5B from the crenarchaeon Aeropyrum pernixMurakami, Ryo / Miyoshi, Tomohiro / Uchiumi, Toshio / Ito, Kosuke et al. | 2016
- 721
-
Universal features of fluctuations in globular proteinsErman, Burak et al. | 2016
- 726
-
Identification of putative unfolding intermediates of the mutant His‐107‐tyr of human carbonic anhydrase II in a multidimensional property spaceHalder, Puspita / Taraphder, Srabani et al. | 2016
- 744
-
Crystal structure of the deglycating enzyme Amadoriase I in its free form and substrate‐bound complexRigoldi, Federica / Gautieri, Alfonso / Dalle Vedove, Andrea / Lucarelli, Anna Paola / Vesentini, Simone / Parisini, Emilio et al. | 2016
- 759
-
Crystal structures of OprN and OprJ, outer membrane factors of multidrug tripartite efflux pumps of Pseudomonas aeruginosaYonehara, Ryo / Yamashita, Eiki / Nakagawa, Atsushi et al. | 2016
- 770
-
Prior knowledge or freedom of interpretation? A critical look at a recently published classification of “novel” Zn binding sitesRaczynska, Joanna E / Wlodawer, Alexander / Jaskolski, Mariusz et al. | 2016
- 777
-
Coarse‐grained modeling of the intrinsically disordered protein Histatin 5 in solution: Monte Carlo simulations in combination with SAXSCragnell, Carolina / Durand, Dominique / Cabane, Bernard / Skepö, Marie et al. | 2016
- 792
-
Identification of the active site of human mitochondrial malonyl‐coenzyme a decarboxylase: A combined computational studyLing, Baoping / Liu, Yuxia / Li, Xiaoping / Wang, Zhiguo / Bi, Siwei et al. | 2016
- 803
-
Protein side chain conformation predictions with an MMGBSA energy functionGaillard, Thomas / Panel, Nicolas / Simonson, Thomas et al. | 2016
- 820
-
Pressure‐induced conformational switch of an interfacial proteinJohnson, Quentin R. / Lindsay, Richard J. / Nellas, Ricky B. / Shen, Tongye et al. | 2016
- 828
-
Purine salvage in Methanocaldococcus jannaschii: Elucidating the role of a conserved cysteine in adenine deaminaseMiller, Danielle V. / Brown, Anne M. / Xu, Huimin / Bevan, David R. / White, Robert H. et al. | 2016
- 841
-
Dissecting the roles of local packing density and longer‐range effects in protein sequence evolutionShahmoradi, Amir / Wilke, Claus O. et al. | 2016
- 855
-
Structural basis for cellulose binding by the type A carbohydrate‐binding module 64 of Spirochaeta thermophilaSchiefner, André / Angelov, Angel / Liebl, Wolfgang / Skerra, Arne et al. | 2016
- 859
-
Structural and biochemical insights into 7[beta]-hydroxysteroid dehydrogenase stereoselectivitySimone Savino et al. | 2016
- 859
-
Structural and biochemical insights into 7β‐hydroxysteroid dehydrogenase stereoselectivitySavino, Simone / Ferrandi, Erica Elisa / Forneris, Federico / Rovida, Stefano / Riva, Sergio / Monti, Daniela / Mattevi, Andrea et al. | 2016
- 869
-
ScaffoldSeq: Software for characterization of directed evolution populationsWoldring, Daniel R. / Holec, Patrick V. / Hackel, Benjamin J. et al. | 2016
- 875
-
Molecular dynamics simulations of apo, holo, and inactivator bound GABA‐at reveal the role of active site residues in PLP dependent enzymesGökcan, Hatice / Monard, Gerald / Sungur Konuklar, F. Aylin et al. | 2016
- 892
-
Structural analysis of the active site architecture of the VapC toxin from Shigella flexneriXu, Kehan / Dedic, Emil / Brodersen, Ditlev E. et al. | 2016
- 900
-
Understanding the physical basis for the side‐chain conformational preferences of methionineVirrueta, Alejandro / O'Hern, Corey S. / Regan, Lynne et al. | 2016
- 912
-
Solution structure of TbTFIIS2‐1 PWWP domain from Trypanosoma bruceiWang, Rui / Zhang, Jiahai / Liao, Shanhui / Tu, Xiaoming et al. | 2016
- 920
-
Interplay between binding affinity and kinetics in protein–protein interactionsCao, Huaiqing / Huang, Yongqi / Liu, Zhirong et al. | 2016
- 934
-
Structural determinants in bacterial 2‐keto‐3‐deoxy‐D‐gluconate dehydrogenase KduD for dual‐coenzyme specificityTakase, Ryuichi / Maruyama, Yukie / Oiki, Sayoko / Mikami, Bunzo / Murata, Kousaku / Hashimoto, Wataru et al. | 2016
- 948
-
Comprehensive analysis of motions in molecular dynamics trajectories of the actin capping protein and its inhibitor complexesKoike, Ryotaro / Takeda, Shuichi / Maéda, Yuichiro / Ota, Motonori et al. | 2016
- 957
-
Conservation of structural fluctuations in homologous protein kinases and its implications on functional sitesKalaivani, Raju / de Brevern, Alexandre G. / Srinivasan, Narayanaswamy et al. | 2016
- 979
-
Surface shapes and surrounding environment analysis of single‐ and double‐stranded DNA‐binding proteins in protein‐DNA interfaceWang, Wei / Liu, Juan / Sun, Lin et al. | 2016
- 990
-
Mechanism of allosteric propagation across a β‐sheet structure investigated by molecular dynamics simulationsInterlandi, Gianluca / Thomas, Wendy E. et al. | 2016
- 990
-
Mechanism of allosteric propagation across a [beta]-sheet structure investigated by molecular dynamics simulationsGianluca Interlandi et al. | 2016
- 1009
-
Folding superfunnel to describe cooperative folding of interacting proteinsSmeller, László et al. | 2016
- 1021
-
MQAPsingle: A quasi single‐model approach for estimation of the quality of individual protein structure modelsPawlowski, Marcin et al. | 2016
- 1029
-
The crystal structure of maleylacetate reductase from Rhizobium sp. strain MTP‐10005 provides insights into the reaction mechanism of enzymes in its original familyFujii, Tomomi et al. | 2016
- 1043
-
Synergistic enhancement of cellulase pairs linked by consensus ankyrin repeats: Determination of the roles of spacing, orientation, and enzyme identityCunha, Eva S et al. | 2016
- 1055
-
Probing the structural dynamics of the SNARE recycling machine based on coarse‐grained modelingZheng, Wenjun et al. | 2016
- 1067
-
Coarse‐grained simulations of proton‐dependent conformational changes in lactose permeaseJewel, Yead et al. | 2016
- 1075
-
The SCP2‐thiolase‐like protein (SLP) of Trypanosoma brucei is an enzyme involved in lipid metabolismHarijan, Rajesh K et al. | 2016
- 1097
-
NMR identification of the binding surfaces involved in the Salmonella and Shigella Type III secretion tip‐translocon protein–protein interactionsMcShan, Andrew C et al. | 2016
- 1108
-
Insights into mechanism of pyrido[2,3‐d]pyrimidines as DYRK1A inhibitors based on molecular dynamic simulationsLi, Jiao Jiao et al. | 2016
- 1124
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Intrinsic disorder accelerates dissociation rather than associationUmezawa, Koji et al. | 2016
- 1134
-
Replica exchange molecular dynamics simulation of cross‐fibrillation of IAPP and PrP106‐126Chua, Khi Pin et al. | 2016
- 1147
-
Statistical analysis of structural determinants for protein–DNA‐binding specificityCorona, Rosario I et al. | 2016
- 1162
-
Structural analysis of nested neutralizing and non‐neutralizing B cell epitopes on ricin toxin's enzymatic subunitRudolph, Michael J et al. | 2016
- 1177
-
Molprobity's ultimate rotamer‐library distributions for model validationHintze, Bradley J. / Lewis, Steven M. / Richardson, Jane S. / Richardson, David C. et al. | 2016
- 1190
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Comparative analyses of quaternary arrangements in homo‐oligomeric proteins in superfamilies: Functional implicationsSudha, Govindarajan / Srinivasan, Narayanaswamy et al. | 2016
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Characterization of the flexibility of the peripheral stalk of prokaryotic rotary A‐ATPases by atomistic simulationsPapachristos, Kostas / Muench, Stephen P. / Paci, Emanuele et al. | 2016
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Hydrophobic tail length plays a pivotal role in amyloid beta (25–35) fibril–surfactant interactionsBag, Sudipta / Chaudhury, Susmitnarayan / Pramanik, Dibyendu / DasGupta, Sunando / Dasgupta, Swagata et al. | 2016
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GGIP: Structure and sequence‐based GPCR–GPCR interaction pair predictorNemoto, Wataru / Yamanishi, Yoshihiro / Limviphuvadh, Vachiranee / Saito, Akira / Toh, Hiroyuki et al. | 2016
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Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometryAl‐Eryani, Yusra / Ib Rasmussen, Morten / Kjellström, Sven / Højrup, Peter / Emanuelsson, Cecilia / von Wachenfeldt, Claes et al. | 2016
- 1246
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Structures of paraoxon‐inhibited human acetylcholinesterase reveal perturbations of the acyl loop and the dimer interfaceFranklin, Matthew C. / Rudolph, Michael J. / Ginter, Christopher / Cassidy, Michael S. / Cheung, Jonah et al. | 2016
- 1257
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Fe2+ binding on amyloid [beta]-peptide promotes aggregationSubramaniam Boopathi et al. | 2016
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Fe2+ binding on amyloid β‐peptide promotes aggregationBoopathi, Subramaniam / Kolandaivel, Ponmalai et al. | 2016
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The volume of cavities in proteins and virus capsidsChwastyk, Mateusz / Jaskolski, Mariusz / Cieplak, Marek et al. | 2016
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Mechanism for verification of mismatched and homoduplex DNAs by nucleotides‐bound MutS analyzed by molecular dynamics simulationsIshida, Hisashi / Matsumoto, Atsushi et al. | 2016
- 1304
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Solution structure of the lymphocyte receptor Nkrp1a reveals a distinct conformation of the long loop region as compared to in the crystal structureRozbeský, Daniel / Adámek, David / Pospíšilová, Eliška / Novák, Petr / Chmelík, Josef et al. | 2016
- 1312
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Protein–protein structure prediction by scoring molecular dynamics trajectories of putative posesSarti, Edoardo / Gladich, Ivan / Zamuner, Stefano / Correia, Bruno E. / Laio, Alessandro et al. | 2016
- 1321
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Crystal structure of a [NiFe] hydrogenase maturation protease HybD from Thermococcus kodakarensis KOD1Kwon, Sunghark / Nishitani, Yuichi / Watanabe, Satoshi / Hirao, Yoshinori / Imanaka, Tadayuki / Kanai, Tamotsu / Atomi, Haruyuki / Miki, Kunio et al. | 2016
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SH3‐like motif‐containing C‐terminal domain of staphylococcal teichoic acid transporter suggests possible functionKo, Tzu‐Ping / Tseng, Shih‐Ting / Lai, Shu‐Jung / Chen, Sheng‐Chia / Guan, Hong‐Hsiang / Shin Yang, Chia / Jung Chen, Chun / Chen, Yeh et al. | 2016
- 1333
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Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategyStamm, Marcus / Forrest, Lucy R. et al. | 2016
- 1334
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Solution structure and interface‐driven self‐assembly of NC2, a new member of the Class II hydrophobin proteinsRen, Qin / Kwan, Ann H. / Sunde, Margaret et al. | 2016
- 1339
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Mutation design of a thermophilic Rubisco based on three‐dimensional structure enhances its activity at ambient temperatureFujihashi, Masahiro / Nishitani, Yuichi / Kiriyama, Tomohiro / Aono, Riku / Sato, Takaaki / Takai, Tomoyuki / Tagashira, Kenta / Fukuda, Wakao / Atomi, Haruyuki / Imanaka, Tadayuki et al. | 2016
- 1347
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Dowser++, a new method of hydrating protein structuresMorozenko, A. / Stuchebrukhov, A. A. et al. | 2016
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Artificial proteins as allosteric modulators of PDZ3 and SH3 in two‐domain constructs: A computational characterization of novel chimeric proteinsKirubakaran, Palani / Pfeiferová, Lucie / Boušová, Kristýna / Bednarova, Lucie / Obšilová, Veronika / Vondrášek, Jiří et al. | 2016
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Structural characterization of the heme‐based oxygen sensor, AfGcHK, its interactions with the cognate response regulator, and their combined mechanism of action in a bacterial two‐component signaling systemStranava, Martin / Martínek, Václav / Man, Petr / Fojtikova, Veronika / Kavan, Daniel / Vaněk, Ondřej / Shimizu, Toru / Martinkova, Marketa et al. | 2016
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BiPPred: Combined sequence‐ and structure‐based prediction of peptide binding to the Hsp70 chaperone BiPSchneider, Markus / Rosam, Mathias / Glaser, Manuel / Patronov, Atanas / Shah, Harpreet / Back, Katrin Christiane / Daake, Marina Angelika / Buchner, Johannes / Antes, Iris et al. | 2016
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Great interactions: How binding incorrect partners can teach us about protein recognition and functionVamparys, Lydie / Laurent, Benoist / Carbone, Alessandra / Sacquin‐Mora, Sophie et al. | 2016
- 1422
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Characterization of the structure and catalytic activity of Legionella pneumophila VipFYoung, Byron H. / Caldwell, Tracy A. / McKenzie, Aidan M. / Kokhan, Oleksandr / Berndsen, Christopher E. et al. | 2016
- 1431
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Potential DNA binding and nuclease functions of ComEC domains characterized in silicoBaker, James A. / Simkovic, Felix / Taylor, Helen M.C. / Rigden, Daniel J. et al. | 2016
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Reactivation of mutant p53: Constraints on mechanism highlighted by principal component analysis of the DNA binding domainOuaray, Zahra / ElSawy, Karim M. / Lane, David P. / Essex, Jonathan W. / Verma, Chandra et al. | 2016
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The part of a long beta hairpin from the scrapie form of the human prion protein is reconstructed in the synthetic CC36 proteinKhrustalev, Vladislav Victorovich / Khrustaleva, Tatyana Aleksandrovna / Szpotkowski, Kamil / Poboinev, Victor Vitoldovich / Kakhanouskaya, Katsiaryna Yurieuna et al. | 2016
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Accelerated molecular dynamics simulations of the octopamine receptor using GPUs: discovery of an alternate agonist‐binding positionKastner, Kevin W. / Izaguirre, Jesús A. et al. | 2016
- 1490
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FF12MC: A revised AMBER forcefield and new protein simulation protocolPang, Yuan‐Ping et al. | 2016
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Novel proteases from the genome of the carnivorous plant Drosera capensis: Structural prediction and comparative analysisButts, Carter T. / Bierma, Jan C. / Martin, Rachel W. et al. | 2016
- 1534
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Computational exploration of the binding mode of heme‐dependent stimulators into the active catalytic domain of soluble guanylate cyclaseAgulló, Luis / Buch, Ignasi / Gutiérrez‐de‐Terán, Hugo / Garcia‐Dorado, David / Villà‐Freixa, Jordi et al. | 2016
- 1549
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THz frequency spectrum of protein–solvent interaction energy using a recurrence plot‐based Wiener–Khinchin methodKarain, Wael et al. | 2016
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Crystal structure of the N‐terminal domain of human SIRT7 reveals a three‐helical domain architecturePriyanka, Anu / Solanki, Vipul / Parkesh, Raman / Thakur, Krishan Gopal et al. | 2016
- 1567
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Conformational flexibility of the complete catalytic domain of Cdc25B phosphatasesSayegh, Raphael S. R et al. | 2016
- 1576
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Amino acid function relates to its embedded protein microenvironment: A study on disulfide-bridged cystineBhatnagar, Akshay et al. | 2016
- 1590
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Processivity of nucleic acid unwinding and translocation by helicasesXie, Ping et al. | 2016
- 1606
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QM/MM studies on the calcium-assisted [beta]-elimination mechanism of pectate lyase from bacillus subtilisGuangcai Ma et al. | 2016
- 1606
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QM/MM studies on the calcium-assisted β-elimination mechanism of pectate lyase from bacillus subtilisMa, Guangcai et al. | 2016
- 1616
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The control of the discrimination between dNTP and rNTP in DNA and RNA polymeraseYoon, Hanwool et al. | 2016
- 1625
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Structural mutation analysis of PTEN and its genotype-phenotype correlations in endometriosis and cancerIris N Smith et al. | 2016
- 1644
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Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase [beta]Ricardo A Matute et al. | 2016
- 1644
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Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase βMatute, Ricardo A et al. | 2016
- 1658
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Role of W181 in modulating kinetic properties of Plasmodium falciparum hypoxanthine guanine xanthine phosphoribosyltransferaseRoy, Sourav et al. | 2016
- 1670
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Analysis of proton wires in the enzyme active site suggests a mechanism of c-di-GMP hydrolysis by the EAL domain phosphodiesterasesGrigorenko, Bella L et al. | 2016
- 1681
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The crystal structure of Clostridium perfringens SleM, a muramidase involved in cortical hydrolysis during spore germinationAl-Riyami, Bahja et al. | 2016
- 1690
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Mechanisms for allosteric activation of protease DegS by ligand binding and oligomerization as revealed from molecular dynamics simulationsLu, Cheng et al. | 2016
- 1706
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TMSEG: Novel prediction of transmembrane helicesBernhofer, Michael et al. | 2016
- 1717
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Molecular aspects of the interaction between Mason-Pfizer monkey virus matrix protein and artificial phospholipid membraneJunková, P et al. | 2016
- 1728
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Structure-based classification of FAD binding sites: A comparative study of structural alignment toolsLeonardo D Garma et al. | 2016
- 1748
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Solution NMR structures of the C-domain of Tetrahymena cytoskeletal protein Tcb2 reveal distinct calcium-induced structural rearrangementsKilpatrick, Adina M et al. | 2016
- 1761
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Structural basis of reversine selectivity in inhibiting Mps1 more potently than aurora B kinaseHiruma, Yoshitaka / Koch, Andre / Dharadhar, Shreya / Joosten, Robbie P. / Perrakis, Anastassis et al. | 2016
- 1767
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Temperature‐induced unfolding behavior of proteins studied by tensorial elastic network modelSrivastava, Amit / Granek, Rony et al. | 2016
- 1776
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The flexibility and dynamics of protein disulfide isomeraseRömer, Rudolf A. / Wells, Stephen A. / Emilio Jimenez‐Roldan, J. / Bhattacharyya, Moitrayee / Vishweshwara, Saraswathi / Freedman, Robert B. et al. | 2016
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Unique coenzyme binding mode of hyperthermophilic archaeal sn‐glycerol‐1‐phosphate dehydrogenase from Pyrobaculum calidifontisHayashi, Junji / Yamamoto, Kaori / Yoneda, Kazunari / Ohshima, Toshihisa / Sakuraba, Haruhiko et al. | 2016
- 1797
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Cofactors‐loaded quaternary structure of lysine‐specific demethylase 5C (KDM5C) protein: Computational modelPeng, Yunhui / Alexov, Emil et al. | 2016
- 1810
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Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix familyNguyen, Vi N. / Park, Annsea / Xu, Anting / Srouji, John R. / Brenner, Steven E. / Kirsch, Jack F. et al. | 2016
- 1823
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Predicting the functional motions of p97 using symmetric normal modesNa, Hyuntae / Song, Guang et al. | 2016
- 1836
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The role of electrostatics in TrxR electron transfer mechanism: A computational approachTeixeira, Vitor H. / Capacho, Ana Sofia C. / Machuqueiro, Miguel et al. | 2016
- 1844
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Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation propertiesTong, Rudi / Wade, Rebecca C. / Bruce, Neil J. et al. | 2016
- 1859
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Development of a motif‐based topology‐independent structure comparison method to identify evolutionarily related foldsDybas, Joseph M. / Fiser, Andras et al. | 2016
- 1875
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Molecular modeling and redesign of alginate lyase from Pseudomonas aeruginosa for accelerating CRPA biofilm degradationCho, Hoon / Huang, Xiaoqin / Lan Piao, Yu / Eun Kim, Da / Yeon Lee, So / Jeong Yoon, Eun / Hee Park, So / Lee, Kyoung / Ho Jang, Chul / Zhan, Chang‐Guo et al. | 2016
- 1888
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Detecting the native ligand orientation by interfacial rigidity: SiteInterlockRaschka, Sebastian / Bemister‐Buffington, Joseph / Kuhn, Leslie A. et al. | 2016
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A multi‐resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand‐binding siteFogarty, Aoife C. / Potestio, Raffaello / Kremer, Kurt et al. | 2016
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Determination of binding affinity upon mutation for type I dockerin–cohesin complexes from Clostridium thermocellum and Clostridium cellulolyticum using deep sequencingKowalsky, Caitlin A. / Whitehead, Timothy A. et al. | 2016
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Three pairs of weak interactions precisely regulate the G‐loop gate of Kir2.1 channelLi, Junwei / Xiao, Shaoying / Xie, Xiaoxiao / Zhou, Hui / Pang, Chunli / Li, Shanshan / Zhang, Hailin / Logothetis, Diomedes E. / Zhan, Yong / An, Hailong et al. | 2016
- 1938
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Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulationWen, Han / Qin, Feng / Zheng, Wenjun et al. | 2016
- C1
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Cover Image, Volume 84, Issue 9Hintze, Bradley J. / Lewis, Steven M. / Richardson, Jane S. / Richardson, David C. et al. | 2016
- C1
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Cover Image, Volume 84, Issue 4Jeschke, Gunnar et al. | 2016
- C1
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Cover Image, Volume 84, Issue 11Lu, Cheng et al. | 2016
- C1
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Cover Image, Volume 84, Issue S1Moult, John / Fidelis, Krzysztof / Kryshtafovych, Andriy / Schwede, Torsten / Tramontano, Anna et al. | 2016
- C1
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Cover Image, Volume 84, Issue 12Hayashi, Junji / Yamamoto, Kaori / Yoneda, Kazunari / Ohshima, Toshihisa / Sakuraba, Haruhiko et al. | 2016
- C1
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Cover Image, Volume 84, Issue 5Deriu, Marco A. / Grasso, Gianvito / Tuszynski, Jack A. / Massai, Diana / Gallo, Diego / Morbiducci, Umberto / Danani, Andrea et al. | 2016
- C1
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Cover Image, Volume 84, Issue 7Kalaivani, Raju / de Brevern, Alexandre G. / Srinivasan, Narayanaswamy et al. | 2016
- C4
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Cover Image, Volume 84, Issue 8Ishida, Hisashi / Matsumoto, Atsushi et al. | 2016
- C1
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Cover Image, Volume 84, Issue 10Butts, Carter T. / Bierma, Jan C. / Martin, Rachel W. et al. | 2016
- C1
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Cover Image, Volume 84, Issue 6Rigoldi, Federica / Gautieri, Alfonso / Dalle Vedove, Andrea / Lucarelli, Anna Paola / Vesentini, Simone / Parisini, Emilio et al. | 2016
- i
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Cover Image, Volume 84, Issue 3Slama, Patrick et al. | 2016
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Issue Information ‐ Cover Image| 2016