Works matching IS 08873585 AND DT 2018 AND VI 86 AND IP 1

Results: 50

Issue Information ‐ Forthcoming.

Published in:: Proteins, 2018, v. 86, n. 1, p. 399, doi. 10.1002/prot.25478
Publication type:: Article

Cover Image, Volume 86, Issue S1.

Published in:

Proteins, 2018, v. 86, n. 1, p. C1, doi. 10.1002/prot.25475

By:

Schaarschmidt, Joerg;
Monastyrskyy, Bohdan;
Kryshtafovych, Andriy;
Bonvin, Alexandre M. J. J.

Publication type:

Article

Issue Information ‐ Table of Content.

Published in:: Proteins, 2018, v. 86, n. 1, p. 1, doi. 10.1002/prot.25436
Publication type:: Article

Data‐assisted protein structure modeling by global optimization in CASP12.

Published in:

Proteins, 2018, v. 86, n. 1, p. 240, doi. 10.1002/prot.25457

By:

Joo, Keehyoung;
Heo, Seungryong;
Joung, InSuk;
Hong, Seung Hwan;
Lee, Sung Jong;
Lee, Jooyoung

Publication type:

Article

Evaluation of the template‐based modeling in CASP12.

Published in:

Proteins, 2018, v. 86, n. 1, p. 321, doi. 10.1002/prot.25425

By:

Kryshtafovych, Andriy;
Monastyrskyy, Bohdan;
Fidelis, Krzysztof;
Moult, John;
Schwede, Torsten;
Tramontano, Anna

Publication type:

Article

Assessment of data‐assisted prediction by inclusion of crosslinking/mass‐spectrometry and small angle X‐ray scattering data in the 12<sup>th</sup> Critical Assessment of protein Structure Prediction experiment.

Published in:

Proteins, 2018, v. 86, n. 1, p. 215, doi. 10.1002/prot.25442

By:

Tamò, Giorgio E.;
Abriata, Luciano A.;
Fonti, Giulia;
Dal Peraro, Matteo

Publication type:

Article

Prediction of protein structure with the coarse‐grained UNRES force field assisted by small X‐ray scattering data and knowledge‐based information.

Published in:

Proteins, 2018, v. 86, n. 1, p. 228, doi. 10.1002/prot.25421

By:

Karczyńska, Agnieszka S.;
Mozolewska, Magdalena A.;
Krupa, Paweł;
Giełdoń, Artur;
Liwo, Adam;
Czaplewski, Cezary

Publication type:

Article

Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12.

Published in:

Proteins, 2018, v. 86, n. 1, p. 387, doi. 10.1002/prot.25431

By:

Haas, Jürgen;
Barbato, Alessandro;
Behringer, Dario;
Studer, Gabriel;
Roth, Steven;
Bertoni, Martino;
Mostaguir, Khaled;
Gumienny, Rafal;
Schwede, Torsten

Publication type:

Article

Protein structure modeling and refinement by global optimization in CASP12.

Published in:

Proteins, 2018, v. 86, n. 1, p. 122, doi. 10.1002/prot.25426

By:

Hong, Seung Hwan;
Joung, InSuk;
Flores‐Canales, Jose C.;
Manavalan, Balachandran;
Cheng, Qianyi;
Heo, Seungryong;
Kim, Jong Yun;
Lee, Sun Young;
Nam, Mikyung;
Joo, Keehyoung;
Lee, In‐Ho;
Lee, Sung Jong;
Lee, Jooyoung

Publication type:

Article

Small angle X‐ray scattering and cross‐linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy.

Published in:

Proteins, 2018, v. 86, n. 1, p. 202, doi. 10.1002/prot.25452

By:

Ogorzalek, Tadeusz L.;
Hura, Greg L.;
Belsom, Adam;
Burnett, Kathryn H.;
Kryshtafovych, Andriy;
Tainer, John A.;
Rappsilber, Juri;
Tsutakawa, Susan E.;
Fidelis, Krzysztof

Publication type:

Article

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment‐based contact prediction methods.

Published in:

Proteins, 2018, v. 86, n. 1, p. 97, doi. 10.1002/prot.25423

By:

Abriata, Luciano A.;
Tamò, Giorgio E.;
Monastyrskyy, Bohdan;
Kryshtafovych, Andriy;
Dal Peraro, Matteo

Publication type:

Article

Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments.

Published in:

Proteins, 2018, v. 86, n. 1, p. 274, doi. 10.1002/prot.25432

By:

Nakamura, Tsukasa;
Oda, Toshiyuki;
Fukasawa, Yoshinori;
Tomii, Kentaro

Publication type:

Article

The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment.

Published in:

Proteins, 2018, v. 86, n. 1, p. 257, doi. 10.1002/prot.25419

By:

Lensink, Marc F.;
Velankar, Sameer;
Baek, Minkyung;
Heo, Lim;
Seok, Chaok;
Wodak, Shoshana J.

Publication type:

Article

Critical assessment of methods of protein structure prediction (CASP)—Round XII.

Published in:

Proteins, 2018, v. 86, n. 1, p. 7, doi. 10.1002/prot.25415

By:

Moult, John;
Fidelis, Krzysztof;
Kryshtafovych, Andriy;
Schwede, Torsten;
Tramontano, Anna

Publication type:

Article

Template‐based and free modeling of I‐TASSER and QUARK pipelines using predicted contact maps in CASP12.

Published in:

Proteins, 2018, v. 86, n. 1, p. 136, doi. 10.1002/prot.25414

By:

Zhang, Chengxin;
Mortuza, S. M.;
He, Baoji;
Wang, Yanting;
Zhang, Yang

Publication type:

Article

Assessment of the model refinement category in CASP12.

Published in:

Proteins, 2018, v. 86, n. 1, p. 152, doi. 10.1002/prot.25409

By:

Hovan, Ladislav;
Oleinikovas, Vladimiras;
Yalinca, Havva;
Kryshtafovych, Andriy;
Saladino, Giorgio;
Gervasio, Francesco Luigi

Publication type:

Article

Assessment of protein assembly prediction in CASP12.

Published in:

Proteins, 2018, v. 86, n. 1, p. 247, doi. 10.1002/prot.25408

By:

Lafita, Aleix;
Bliven, Spencer;
Kryshtafovych, Andriy;
Bertoni, Martino;
Monastyrskyy, Bohdan;
Duarte, Jose M.;
Schwede, Torsten;
Capitani, Guido

Publication type:

Article

Assessment of contact predictions in CASP12: Co‐evolution and deep learning coming of age.

Published in:

Proteins, 2018, v. 86, n. 1, p. 51, doi. 10.1002/prot.25407

By:

Schaarschmidt, Joerg;
Monastyrskyy, Bohdan;
Kryshtafovych, Andriy;
Bonvin, Alexandre M. J. J.

Publication type:

Article

A tribute to Anna Tramontano (1957–2017).

Published in:

Proteins, 2018, v. 86, n. 1, p. 5, doi. 10.1002/prot.25406

By:

Moult, John;
Fidelis, Krzysztof;
Kryshtafovych, Andriy;
Schwede, Torsten

Publication type:

Article

Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.

Published in:

Proteins, 2018, v. 86, n. 1, p. 84, doi. 10.1002/prot.25405

By:

Adhikari, Badri;
Hou, Jie;
Cheng, Jianlin

Publication type:

Article

Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment.

Published in:

Proteins, 2018, v. 86, n. 1, p. 168, doi. 10.1002/prot.25404

By:

Lee, Gyu Rie;
Heo, Lim;
Seok, Chaok

Publication type:

Article

Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi‐automated metrics.

Published in:

Proteins, 2018, v. 86, n. 1, p. 16, doi. 10.1002/prot.25403

By:

Abriata, Luciano A.;
Kinch, Lisa N.;
Tamò, Giorgio E.;
Monastyrskyy, Bohdan;
Kryshtafovych, Andriy;
Dal Peraro, Matteo

Publication type:

Article

Biological and functional relevance of CASP predictions.

Published in:

Proteins, 2018, v. 86, n. 1, p. 374, doi. 10.1002/prot.25396

By:

Liu, Tianyun;
Ish‐Shalom, Shirbi;
Torng, Wen;
Lafita, Aleix;
Bock, Christian;
Mort, Matthew;
Cooper, David N.;
Bliven, Spencer;
Capitani, Guido;
Mooney, Sean D.;
Altman, Russ B.

Publication type:

Article

Methods for estimation of model accuracy in CASP12.

Published in:

Proteins, 2018, v. 86, n. 1, p. 361, doi. 10.1002/prot.25395

By:

Elofsson, Arne;
Joo, Keehyoung;
Keasar, Chen;
Lee, Jooyoung;
Maghrabi, Ali H. A.;
Manavalan, Balachandran;
McGuffin, Liam J.;
Ménendez Hurtado, David;
Mirabello, Claudio;
Pilstål, Robert;
Sidi, Tomer;
Uziela, Karolis;
Wallner, Björn

Publication type:

Article

What makes it difficult to refine protein models further via molecular dynamics simulations?

Published in:

Proteins, 2018, v. 86, n. 1, p. 177, doi. 10.1002/prot.25393

By:

Heo, Lim;
Feig, Michael

Publication type:

Article

Target highlights from the first post‐PSI CASP experiment (CASP12, May–August 2016).

Published in:

Proteins, 2018, v. 86, n. 1, p. 27, doi. 10.1002/prot.25392

By:

Kryshtafovych, Andriy;
Albrecht, Reinhard;
Baslé, Arnaud;
Bule, Pedro;
Caputo, Alessandro T.;
Carvalho, Ana Luisa;
Chao, Kinlin L.;
Diskin, Ron;
Fidelis, Krzysztof;
Fontes, Carlos M. G. A.;
Fredslund, Folmer;
Gilbert, Harry J.;
Goulding, Celia W.;
Hartmann, Marcus D.;
Hayes, Christopher S.;
Herzberg, Osnat;
Hill, Johan C.;
Joachimiak, Andrzej;
Kohring, Gert‐Wieland;
Koning, Roman I.

Publication type:

Article

Protein structure prediction using Rosetta in CASP12.

Published in:

Proteins, 2018, v. 86, n. 1, p. 113, doi. 10.1002/prot.25390

By:

Ovchinnikov, Sergey;
Park, Hahnbeom;
Kim, David E.;
DiMaio, Frank;
Baker, David

Publication type:

Article

Automatic structure prediction of oligomeric assemblies using Robetta in CASP12.

Published in:

Proteins, 2018, v. 86, n. 1, p. 283, doi. 10.1002/prot.25387

By:

Park, Hahnbeom;
Kim, David E.;
Ovchinnikov, Sergey;
Baker, David;
DiMaio, Frank

Publication type:

Article

Modeling CAPRI targets 110‐120 by template‐based and free docking using contact potential and combined scoring function.

Published in:

Proteins, 2018, v. 86, n. 1, p. 302, doi. 10.1002/prot.25380

By:

Kundrotas, Petras J.;
Anishchenko, Ivan;
Badal, Varsha D.;
Das, Madhurima;
Dauzhenka, Taras;
Vakser, Ilya A.

Publication type:

Article

Improved protein contact predictions with the MetaPSICOV2 server in CASP12.

Published in:

Proteins, 2018, v. 86, n. 1, p. 78, doi. 10.1002/prot.25379

By:

Buchan, Daniel W. A.;
Jones, David T.

Publication type:

Article

Modeling of protein complexes in CAPRI Round 37 using template‐based approach combined with model selection.

Published in:

Proteins, 2018, v. 86, n. 1, p. 292, doi. 10.1002/prot.25378

By:

Dapkūnas, Justas;
Olechnovič, Kliment;
Venclovas, Česlovas

Publication type:

Article

Analysis of deep learning methods for blind protein contact prediction in CASP12.

Published in:

Proteins, 2018, v. 86, n. 1, p. 67, doi. 10.1002/prot.25377

By:

Wang, Sheng;
Sun, Siqi;
Xu, Jinbo

Publication type:

Article

Improved performance in CAPRI round 37 using LZerD docking and template‐based modeling with combined scoring functions.

Published in:

Proteins, 2018, v. 86, n. 1, p. 311, doi. 10.1002/prot.25376

By:

Peterson, Lenna X.;
Shin, Woong‐Hee;
Kim, Hyungrae;
Kihara, Daisuke

Publication type:

Article

Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent.

Published in:

Proteins, 2018, v. 86, n. 1, p. 189, doi. 10.1002/prot.25373

By:

Terashi, Genki;
Kihara, Daisuke

Publication type:

Article

Assessment of model accuracy estimations in CASP12.

Published in:

Proteins, 2018, v. 86, n. 1, p. 345, doi. 10.1002/prot.25371

By:

Kryshtafovych, Andriy;
Monastyrskyy, Bohdan;
Fidelis, Krzysztof;
Schwede, Torsten;
Tramontano, Anna

Publication type:

Article

Accurate template‐based modeling in CASP12 using the IntFOLD4‐TS, ModFOLD6, and ReFOLD methods.

Published in:

Proteins, 2018, v. 86, n. 1, p. 335, doi. 10.1002/prot.25360

By:

McGuffin, Liam J.;
Shuid, Ahmad N.;
Kempster, Robert;
Maghrabi, Ali H. A.;
Nealon, John O.;
Salehe, Bajuna R.;
Atkins, Jennifer D.;
Roche, Daniel B.

Publication type:

Article

Two-domain analysis of JmjN-JmjC and PHD-JmjC lysine demethylases: Detecting an inter-domain evolutionary stress.

Published in:

Proteins, 2018, v. 86, n. 1, p. 3, doi. 10.1002/prot.25394

By:

Slama, Patrick

Publication type:

Article

Spatial features of proteins related to their phosphorylation and associated structural changes.

Published in:

Proteins, 2018, v. 86, n. 1, p. 13, doi. 10.1002/prot.25397

By:

Karasev, Dmitry A.;
Veselova, Darya A.;
Veselovsky, Alexander V.;
Sobolev, Boris N.;
Zgoda, Victor G.;
Archakov, Alexander I.

Publication type:

Article

Crystal structure of D- glycero- Β-D- manno-heptose-1-phosphate adenylyltransferase from Burkholderia pseudomallei.

Published in:

Proteins, 2018, v. 86, n. 1, p. 124, doi. 10.1002/prot.25398

By:

Park, Jimin;
Kim, Hyojin;
Kim, Suwon;
Lee, Daeun;
Kim, Mi‐Sun;
Shin, Dong Hae

Publication type:

Article

Computational characterization of substrate and product specificities, and functionality of S-adenosylmethionine binding pocket in histone lysine methyltransferases from Arabidopsis, rice and maize.

Published in:

Proteins, 2018, v. 86, n. 1, p. 21, doi. 10.1002/prot.25399

By:

Satish, Mutyala;
Nivya, M. Angel;
Abhishek, Suman;
Nakarakanti, Naveen Kumar;
Shivani, Dixit;
Vani, Madishetti Vinuthna;
Rajakumara, Eerappa

Publication type:

Article

On the effect of mutations in bovine or camel chymosin on the thermodynamics of binding κ-caseins.

Published in:

Proteins, 2018, v. 86, n. 1, p. 75, doi. 10.1002/prot.25410

By:

Ansari, Samiul M.;
Sørensen, Jesper;
Schiøtt, Birgit;
Palmer, David S.

Publication type:

Article

The nuclear DEK interactome supports multi-functionality.

Published in:

Proteins, 2018, v. 86, n. 1, p. 88, doi. 10.1002/prot.25411

By:

Smith, Eric A.;
Krumpelbeck, Eric F.;
Jegga, Anil G.;
Prell, Malte;
Matrka, Marie M.;
Kappes, Ferdinand;
Greis, Kenneth D.;
Ali, Abdullah M.;
Meetei, Amom R.;
Wells, Susanne I.

Publication type:

Article

Mycobacterium tuberculosis UvrB forms dimers in solution and interacts with UvrA in the absence of ligands.

Published in:

Proteins, 2018, v. 86, n. 1, p. 98, doi. 10.1002/prot.25412

By:

Lahiri, Samarpita;
Rizzi, Menico;
Rossi, Franca;
Miggiano, Riccardo

Publication type:

Article

Chaperone-client interactions between Hsp21 and client proteins monitored in solution by small angle X-ray scattering and captured by crosslinking mass spectrometry.

Published in:

Proteins, 2018, v. 86, n. 1, p. 110, doi. 10.1002/prot.25413

By:

Rutsdottir, Gudrun;
I. Rasmussen, Morten;
Hojrup, Peter;
Bernfur, Katja;
Emanuelsson, Cecilia;
Söderberg, Christopher A. G.

Publication type:

Article

Cover Image, Volume 86, Issue 1.

Published in:

Proteins, 2018, v. 86, n. 1, p. C1, doi. 10.1002/prot.25434

By:

Park, Jimin;
Kim, Hyojin;
Kim, Suwon;
Lee, Daeun;
Kim, Mi‐Sun;
Shin, Dong Hae

Publication type:

Article

Issue Information - Table of Content.

Published in:: Proteins, 2018, v. 86, n. 1, p. 1, doi. 10.1002/prot.25436
Publication type:: Article

Cover Image, Volume 86, Issue 1.

Published in:

Proteins, 2018, v. 86, n. 1, p. C4, doi. 10.1002/prot.25437

By:

Koehler Leman, Julia;
D'Avino, Andrew R.;
Bhatnagar, Yash;
Gray, Jeffrey J.

Publication type:

Article

Elastic Surface Model For Beta-Barrels: Geometric, Computational, And Statistical Analysis.

Published in:

Proteins, 2018, v. 86, n. 1, p. 35, doi. 10.1002/prot.25400

By:

Toda, Magdalena;
Zhang, Fangyuan;
Athukorallage, Bhagya

Publication type:

Article

Molecular dynamics simulation, binding free energy calculation and unbinding pathway analysis on selectivity difference between FKBP51 and FKBP52: Insight into the molecular mechanism of isoform selectivity.

Published in:

Proteins, 2018, v. 86, n. 1, p. 43, doi. 10.1002/prot.25401

By:

Shi, Danfeng;
Bai, Qifeng;
Zhou, Shuangyan;
Liu, Xuewei;
Liu, Huanxiang;
Yao, Xiaojun

Publication type:

Article

Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality.

Published in:

Proteins, 2018, v. 86, n. 1, p. 57, doi. 10.1002/prot.25402

By:

Koehler Leman, Julia;
D'Avino, Andrew R.;
Bhatnagar, Yash;
Gray, Jeffrey J.

Publication type:

Article