Works matching AU Fiser, Andras

Results: 52

Predicting disulfide bond connectivity in proteins by correlated mutations analysis.

Published in:

Bioinformatics, 2008, v. 24, n. 4, p. 498, doi. 10.1093/bioinformatics/btm637

By:

Rotem Rubinstein;
Andras Fiser

Publication type:

Article

Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments.

Published in:

Bioinformatics, 2007, v. 23, n. 19, p. 2558, doi. 10.1093/bioinformatics/btm377

By:

Narcis Fernandez-Fuentes;
Brajesh K. Rai;
Carlos J. Madrid-Aliste;
J. Eduardo Fajardo;
András Fiser

Publication type:

Article

MMM: a sequence-to-structure alignment protocol.

Published in:

Bioinformatics, 2006, v. 22, n. 21, p. 2691

By:

András Fiser

Publication type:

Article

EPIC-DB: a proteomics database for studying Apicomplexan organisms.

Published in:

BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-38

By:

Madrid-Aliste, Carlos J.;
Dybas, Joseph M.;
Angeletti, Ruth Hogue;
Weiss, Louis M.;
Kami Kim;
Simon, Istvan;
Fiser, Andras

Publication type:

Article

ModLoop: automated modeling of loops in protein structures.

Published in:

Bioinformatics, 2003, v. 19, n. 18, p. 2500, doi. 10.1093/bioinformatics/btg362

By:

András Fiser

Publication type:

Article

Predicting the oxidation state of cysteines by multiple sequence alignment.

Published in:

Bioinformatics, 2000, v. 16, n. 3, p. 251, doi. 10.1093/bioinformatics/16.3.251

By:

Fiser, András;
Simon, István

Publication type:

Article

Identification and functional validation of an enhancer variant in the 9p21.3 locus associated with glaucoma risk and elevated expression of p16<sup>INK4a</sup>.

Published in:

Aging Cell, 2023, v. 22, n. 9, p. 1, doi. 10.1111/acel.13908

By:

Zhu, Yizhou;
Tazearslan, Cagdas;
Rosenfeld, Michael G.;
Fiser, Andras;
Suh, Yousin

Publication type:

Article

Computational Analysis and Experimental Validation of Gene Predictions in Toxoplasma gondii.

Published in:

PLoS ONE, 2008, v. 3, n. 12, p. 1, doi. 10.1371/journal.pone.0003899

By:

Dybas, Joseph M.;
Madrid-Aliste, Carlos J.;
Fa-Yun Che;
Nieves, Edward;
Rykunov, Dmitry;
Angeletti, Ruth Hogue;
Weiss, Louis M.;
Kim, Kami;
Fiser, Andras

Publication type:

Article

miRNA-mediated loss of m<sup>6</sup>A increases nascent translation in glioblastoma.

Published in:

PLoS Genetics, 2021, v. 17, n. 3, p. 1, doi. 10.1371/journal.pgen.1009086

By:

Zepecki, John P.;
Karambizi, David;
Fajardo, J. Eduardo;
Snyder, Kristin M.;
Guetta-Terrier, Charlotte;
Tang, Oliver Y.;
Chen, Jia-Shu;
Sarkar, Atom;
Fiser, Andras;
Toms, Steven A.;
Tapinos, Nikos

Publication type:

Article

Protein—protein binding supersites.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 01, p. 1, doi. 10.1371/journal.pcbi.1006704

By:

Viswanathan, Raji;
Fajardo, Eduardo;
Steinberg, Gabriel;
Haller, Matthew;
Fiser, Andras

Publication type:

Article

Letter to the Editor: 1H, 13C, 15N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N*.

Published in:

Journal of Biomolecular NMR, 2001, v. 19, n. 3, p. 289, doi. 10.1023/A:1011292919947

By:

Barrientos, Laura G.;
Campos-Olivas, Ramón;
Louis, John M.;
Fiser, András;
Šali, Andrej;
Gronenborn, Angela M.

Publication type:

Article

Smotifs as structural local descriptors of supersecondary elements: classification, completeness and applications.

Published in:

Bio-Algorithms & Med-Systems, 2014, v. 10, n. 4, p. 195, doi. 10.1515/bams-2014-0016

By:

Bonet, Jaume;
Fiser, Andras;
Oliva, Baldo;
Fernandez-Fuentes, Narcis

Publication type:

Article

HIV-Tat regulates macrophage gene expression in the context of neuroAIDS.

Published in:

PLoS ONE, 2017, v. 12, n. 6, p. 1, doi. 10.1371/journal.pone.0179882

By:

Carvallo, Loreto;
Lopez, Lillie;
Jaureguiberry-Bravo, Matias;
Berman, Joan W.;
Fajardo, Jorge E.;
Fiser, Andras

Publication type:

Article

Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials.

Published in:

Proteins, 2007, v. 67, n. 3, p. 559, doi. 10.1002/prot.21279

By:

Rykunov, Dmitry;
Fiser, András

Publication type:

Article

Multiple mapping method: A novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling.

Published in:

Proteins, 2006, v. 63, n. 3, p. 644, doi. 10.1002/prot.20835

By:

Rai, Brajesh K.;
Fiser, András

Publication type:

Article

A word of caution about biological inference – Revisiting cysteine covalent state predictions.

Published in:

FEBS Open Bio, 2014, v. 4, p. 310, doi. 10.1016/j.fob.2014.03.003

By:

Tüdős, Éva;
Mészáros, Bálint;
Fiser, András;
Simon, István

Publication type:

Article

A word of caution about biological inference – Revisiting cysteine covalent state predictions.

Published in:

FEBS Open Bio, 2014, v. 4, n. 1, p. 310, doi. 10.1016/j.fob.2014.03.003

By:

Tüdős, Éva;
Mészáros, Bálint;
Fiser, András;
Simon, István

Publication type:

Article

Pathogenic NAP57 mutations decrease ribonucleoprotein assembly in dyskeratosis congenita.

Published in:

Human Molecular Genetics, 2009, v. 18, n. 23, p. 4546, doi. 10.1093/hmg/ddp416

By:

Grozdanov, Petar N.;
Fernandez-Fuentes, Narcis;
Fiser, Andras;
Meier, U. Thomas

Publication type:

Article

Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 8, p. 1, doi. 10.1371/journal.pcbi.1004419

By:

Vallat, Brinda;
Madrid-Aliste, Carlos;
Fiser, Andras

Publication type:

Article

The Underlying Molecular and Network Level Mechanisms in the Evolution of Robustness in Gene Regulatory Networks.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 1, p. 1, doi. 10.1371/journal.pcbi.1002865

By:

Pujato, Mario;
MacCarthy, Thomas;
Fiser, Andras;
Bergman, Aviv

Publication type:

Article

Structural Characteristics of Novel Protein Folds.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 4, p. 1, doi. 10.1371/journal.pcbi.1000750

By:

Fernandez-Fuentes, Narcis;
Dybas, Joseph M.;
Fiser, Andras

Publication type:

Article

Photo-assisted peptide enrichment in protein complex cross-linking analysis of a model homodimeric protein using mass spectrometry.

Published in:

Proteomics, 2011, v. 11, n. 20, p. 4109, doi. 10.1002/pmic.201100015

By:

Yan, Funing;
Che, Fa-Yun;
Nieves, Edward;
Weiss, Louis M.;
Angeletti, Ruth H.;
Fiser, Andras

Publication type:

Article

Role of the Egr2 Promoter Antisense RNA in Modulating the Schwann Cell Chromatin Landscape.

Published in:

Biomedicines, 2024, v. 12, n. 11, p. 2594, doi. 10.3390/biomedicines12112594

By:

Martinez Moreno, Margot;
Karambizi, David;
Hwang, Hyeyeon;
Fregoso, Kristen;
Michles, Madison J.;
Fajardo, Eduardo;
Fiser, Andras;
Tapinos, Nikos

Publication type:

Article

Transactivation of Abl by the Crk II adapter protein requires a PNAY sequence in the Crk C-terminal SH3 domain.

Published in:

Oncogene, 2005, v. 24, n. 55, p. 8187, doi. 10.1038/sj.onc.1208988

By:

Reichman, Charles;
Singh, Kamalendra;
Yan Liu;
Singh, Sukhwinder;
Hong Li;
Fajardo, J. Eduardo;
Fiser, Andras;
Birge, Raymond B.

Publication type:

Article

Core Histones of the Amitochondriate Protist, Giardia lamblia.

Published in:

Molecular Biology & Evolution, 2000, v. 17, n. 8, p. 1156, doi. 10.1093/oxfordjournals.molbev.a026398

By:

Wu, Gang;
McArthur, Andrew G.;
Fiser, András;
Šali‡, Andrej;
Sogin, Mitchell L.;
M, Miklós

Publication type:

Article

MODBASE, a database of annotated comparative protein structure models, and associated resources.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d217

By:

Pieper, Ursula;
Eswar, Narayanan;
Braberg, Hannes;
Madhusudhan, M. S.;
Davis, Fred P.;
Stuart, Ashley C.;
Mirkovic, Nebojsa;
Rossi, Andrea;
Marti‐Renom, Marc A.;
Fiser, Andras;
Webb, Ben;
Greenblatt, Daniel;
Huang, Conrad C.;
Ferrin, Thomas E.;
Sali, Andrej

Publication type:

Article

Tools for comparative protein structure modeling and analysis.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 13, p. 3375, doi. 10.1093/nar/gkg543

By:

Eswar, Narayanan;
John, Bino;
Mirkovic, Nebojsa;
Fiser, Andras;
Ilyin, Valentin A.;
Pieper, Ursula;
Stuart, Ashley C.;
Marti-Renom, Marc A.;
Madhusudhan, M. S.;
Yerkovich, Bozidar;
Sali, Andrej

Publication type:

Article

Servers for sequence–structure relationship analysis and prediction.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 13, p. 3359, doi. 10.1093/nar/gkg589

By:

Dosztányi, Zsuzsanna;
Magyar, Csaba;
Tusnády, Gábor E.;
Cserző, Miklós;
Fiser, András;
Simon, István

Publication type:

Article

Saturating representation of loop conformational fragments in structure databanks.

Published in:

BMC Structural Biology, 2006, v. 6, p. 15, doi. 10.1186/1472-6807-6-15

By:

Fernandez-Fuentes, Narcis;
Fiser, András

Publication type:

Article

Protein structure based prediction of catalytic residues.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-63

By:

Fajardo, J. Eduardo;
Fiser, Andras

Publication type:

Article

New statistical potential for quality assessment ofprotein models and a survey of energy functions.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 128, doi. 10.1186/1471-2105-11-128

By:

Rykunov, Dmitry;
Fiser, Andras

Publication type:

Article

Computational prediction of multiple antigen epitopes.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae556

By:

Viswanathan, Rajalakshmi;
Carroll, Moshe;
Roffe, Alexandra;
Fajardo, Jorge E;
Fiser, Andras

Publication type:

Article

Optimal selection of suitable templates in protein interface prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad510

By:

Grudman, Steven;
Fajardo, J Eduardo;
Fiser, Andras

Publication type:

Article

INTERCAAT: identifying interface residues between macromolecules.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 554, doi. 10.1093/bioinformatics/btab596

By:

Grudman, Steven;
Fajardo, J Eduardo;
Fiser, Andras

Publication type:

Article

The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis.

Published in:

Bioinformatics, 2019, v. 35, n. 1, p. 12, doi. 10.1093/bioinformatics/bty523

By:

Gil, Nelson;
Fiser, Andras

Publication type:

Article

Identifying functionally informative evolutionary sequence profiles.

Published in:

Bioinformatics, 2018, v. 34, n. 8, p. 1278, doi. 10.1093/bioinformatics/btx779

By:

Gil, Nelson;
Fiser, Andras

Publication type:

Article

Assessing the functional impact of protein binding site definition.

Published in:

Protein Science: A Publication of the Protein Society, 2024, v. 33, n. 6, p. 1, doi. 10.1002/pro.5026

By:

Nandigrami, Prithviraj;
Fiser, Andras

Publication type:

Article

Modeling mutations in protein structures.

Published in:

Protein Science: A Publication of the Protein Society, 2007, v. 16, n. 9, p. 2030, doi. 10.1110/ps.072855507

By:

Feyfant, Eric;
Sali, Andrej;
Fiser, András

Publication type:

Article

Metabolomic Analysis of Patient Plasma Yields Evidence of Plant-Like α-Linolenic Acid Metabolism in Plasmodium falciparum.

Published in:

Journal of Infectious Diseases, 2012, v. 206, n. 2, p. 238, doi. 10.1093/infdis/jis339

By:

Lakshmanan, Viswanathan;
Rhee, Kyu Y.;
Wang, Wei;
Yu, Yiting;
Khafizov, Kamil;
Fiser, Andras;
Wu, Peng;
Ndir, Omar;
Mboup, Souleymane;
Ndiaye, Daouda;
Daily, Johanna P.

Publication type:

Article

Nuc-ErbB3 regulates H3K27me3 levels and HMT activity to establish epigenetic repression during peripheral myelination.

Published in:

Glia (0894-1491), 2016, v. 64, n. 6, p. 977, doi. 10.1002/glia.22977

By:

Ness, Jennifer K.;
Skiles, Amanda A.;
Yap, Eng‐Hui;
Fajardo, Eduardo J.;
Fiser, Andras;
Tapinos, Nikos

Publication type:

Article

Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes.

Published in:

Nucleic Acids Research, 2014, v. 42, n. 22, p. 13500, doi. 10.1093/nar/gku1228

By:

Pujato, Mario;
Kieken, Fabien;
Skiles, Amanda A.;
Tapinos, Nikos;
Fiser, Andras

Publication type:

Article

M4T: a comparative protein structure modeling server.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W363, doi. 10.1093/nar/gkm341

By:

Fernandez-Fuentes, Narcis;
Madrid-Aliste, Carlos J.;
Rai, Brajesh Kumar;
Fajardo, J. Eduardo;
Fiser, András

Publication type:

Article

ArchPRED: a template based loop structure prediction server.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 11, p. w173, doi. 10.1093/nar/gkl113

By:

Fernandez-Fuentes, Narcis;
Zhai, Jun;
Fiser, András

Publication type:

Article

A supersecondary structure library and search algorithm for modeling loops in protein structures.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 7, p. 2085, doi. 10.1093/nar/gkl156

By:

Fernandez-Fuentes, Narcis;
Oliva, Baldomero;
Fiser, András

Publication type:

Article

Modeling of loops in protein structures.

Published in:

Protein Science: A Publication of the Protein Society, 2000, v. 9, n. 9, p. 1753

By:

FISER, ANDRÁS;
DO, RICHARD KINH GIAN;
`ALI, ANDREJ

Publication type:

Article

Estimating the accuracy of pharmacophore‐based detection of cognate receptor‐ligand pairs in the immunoglobulin superfamily.

Published in:

Proteins, 2021, v. 89, n. 6, p. 632, doi. 10.1002/prot.26046

By:

Gil, Nelson;
Shrestha, Rojan;
Fiser, Andras

Publication type:

Article

Discovery of receptor‐ligand interfaces in the immunoglobulin superfamily.

Published in:

Proteins, 2020, v. 88, n. 1, p. 135, doi. 10.1002/prot.25778

By:

Gil, Nelson;
Fajardo, Eduardo J.;
Fiser, Andras

Publication type:

Article

Assessing the accuracy of contact predictions in CASP13.

Published in:

Proteins, 2019, v. 87, n. 12, p. 1058, doi. 10.1002/prot.25819

By:

Shrestha, Rojan;
Fajardo, Eduardo;
Gil, Nelson;
Fidelis, Krzysztof;
Kryshtafovych, Andriy;
Monastyrskyy, Bohdan;
Fiser, Andras

Publication type:

Article

Development of a motif-based topology-independent structure comparison method to identify evolutionarily related folds.

Published in:

Proteins, 2016, v. 84, n. 12, p. 1859, doi. 10.1002/prot.25169

By:

Dybas, Joseph M.;
Fiser, Andras

Publication type:

Article

Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 Å resolution.

Published in:

Proteins, 2010, v. 78, n. 14, p. 3056, doi. 10.1002/prot.22829

By:

Sampathkumar, Parthasarathy;
Lu, Frances;
Zhao, Xun;
Li, Zhenzhen;
Gilmore, Jeremiah;
Bain, Kevin;
Rutter, Marc E.;
Gheyi, Tarun;
Schwinn, Kenneth D.;
Bonanno, Jeffrey B.;
Pieper, Ursula;
Fajardo, J. Eduardo;
Fiser, Andras;
Almo, Steven C.;
Swaminathan, Subramanyam;
Chance, Mark R.;
Baker, David;
Atwell, Shane;
Thompson, Devon A.;
Emtage, J. Spencer

Publication type:

Article