142. Zhu Y, Tazearslan C, Rosenfeld MG, Fiser A, Suh Y
Identification and functional validation of an enhancer variant in the 9p21.3
Aging Cell (2023) 22( 9) : e13908
PMID: 37345431     PMCID: PMC10497822

141. Guetta-Terrier C, Karambizi D, Akosman B, Zepecki JP, Chen JS, Kamle S, Fajardo JE, Fiser A, Singh R, Toms SA, Lee CG, Elias JA, Tapinos N
Chi3l1 Is a Modulator of Glioma Stem Cell States and a Therapeutic Target in
Cancer Res (2023) 83( 12) : 1984-1999
PMID: 37101376     PMCID: PMC10267676

140. Feng M, Namanja-Magliano H, Rajagopalan S, Mishra T, Ducati RG, Hirsch BM, Kelly L, Szymczak W, Fajardo JE, Sidoli S, Fiser A, Jacobs WR, Schramm VL
MAT Gain of Activity Mutation in Helicobacter pylori Is Associated with
ACS Infect Dis (2023) 9( 4) : 966-978
PMID: 36920074     PMCID: PMC10311514

139. Grudman S, Fajardo JE, Fiser A
Optimal selection of suitable templates in protein interface prediction.
Bioinformatics (2023) 39( 9) :
PMID: 37603727     PMCID: PMC10491951

138. Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A
Cell fate decisions, transcription factors and signaling during early retinal
Prog Retin Eye Res (2022) 91, 101093
PMID: 35817658     PMCID: PMC9669153

137. Walder M, Edelstein E, Carroll M, Lazarev S, Fajardo JE, Fiser A, Viswanathan R
Integrated structure-based protein interface prediction.
BMC Bioinformatics (2022) 23( 1) : 301
PMID: 35879651     PMCID: PMC9316365

136. Chidambaram S, Velloso FJ, Rothbard DE, Deshpande K, Cajuste Y, Snyder KM, Fajardo E, Fiser A, Tapinos N, Levison SW, Wood TL
Subventricular zone adult mouse neural stem cells require insulin receptor
Stem Cell Reports (2022) 17( 6) : 1411-1427
PMID: 35523180     PMCID: PMC9213826

135. Grudman S, Fajardo JE, Fiser A
INTERCAAT: identifying interface residues between macromolecules.
Bioinformatics (2022) 38( 2) : 554-555
PMID: 34499117     PMCID: PMC8722752

134. Zepecki JP, Karambizi D, Fajardo JE, Snyder KM, Guetta-Terrier C, Tang OY, Chen JS, Sarkar A, Fiser A, Toms SA, Tapinos N
miRNA-mediated loss of m6A increases nascent translation in glioblastoma.
PLoS Genet (2021) 17( 3) : e1009086
PMID: 33684100     PMCID: PMC7971852

133. Shrestha R, Fajardo JE, Fiser A
Residue-based pharmacophore approaches to study protein-protein interactions.
Curr Opin Struct Biol (2021) 67, 205-211
PMID: 33486430     PMCID: PMC8439153

132. Gil N, Shrestha R, Fiser A
Estimating the accuracy of pharmacophore-based detection of cognate
Proteins (2021) 89( 6) : 632-638
PMID: 33483991     PMCID: PMC8906256

131. Shrestha R, Garrett-Thomson S, Liu W, Almo SC, Fiser A
Allosteric regulation of binding specificity of HVEM for CD160 and BTLA ligands
Curr Res Struct Biol (2021) 3, 337-345
PMID: 34917954     PMCID: PMC8666650

130. Gil N, Fajardo EJ, Fiser A
Discovery of receptor-ligand interfaces in the immunoglobulin superfamily.
Proteins (2020) 88(1) : 135-142
PMID: 31298437     PMCID:

129. Shrestha R, Garrett-Thomson SC, Liu W, Almo SC, Fiser A
Redesigning HVEM Interface for Selective Binding to LIGHT, BTLA, and CD160.
Structure (2020) ,
PMID: 32795404     PMCID:

128. Gil N, Fajardo EJ, Fiser A
Discovery of receptor-ligand interfaces in the immunoglobulin superfamily.
Proteins (2020) 88(1) : 135-142
PMID: 31298437     PMCID: PMC6901748

127. Fajardo JE, Shrestha R, Gil N, Belsom A, Crivelli SN, Czaplewski C, Fidelis K, Grudinin S, Karasikov M, Karczynska AS, Kryshtafovych A, Leitner A, Liwo A, Lubecka EA, Monastyrskyy B, Pages G, Rappsilber J, Sieradzan AK, Sikorska C, Trabjerg E, Fiser A
Assessment of chemical-crosslink-assisted protein structure modeling in CASP13.
Proteins (2020) 88(3) : 540
PMID: 31977133     PMCID:

126. Fajardo JE, Fiser A
A Designer Quest for the Achilles' Heel of Influenza.
Structure (2020) 28(10) : 1083-1084
PMID: 33027689     PMCID:

125. Zhan HQ, Najmi M, Lin K, Aluri S, Fiser A, Goldman ID, Zhao R
A proton-coupled folate transporter mutation causing hereditary folate malabsorption locks the protein in an inward-open conformation.
J Biol Chem (2020) 295(46) : 15650-15661
PMID: 32893190     PMCID: PMC7667981

124. Shrestha R, Garrett-Thomson SC, Liu W, Almo SC, Fiser A
Redesigning HVEM Interface for Selective Binding to LIGHT, BTLA, and CD160.
Structure (2020) 28(11) : 1197-1205.e2
PMID: 32795404     PMCID: PMC7642093

123. Fajardo JE, Shrestha R, Gil N, Belsom A, Crivelli SN, Czaplewski C, Fidelis K, Grudinin S, Karasikov M, Karczynska AS, Kryshtafovych A, Leitner A, Liwo A, Lubecka EA, Monastyrskyy B, Pages G, Rappsilber J, Sieradzan AK, Sikorska C, Trabjerg E, Fiser A
Assessment of chemical-crosslink-assisted protein structure modeling in CASP13.
Proteins (2019) 87(12) : 1283-1297
PMID: 31569265     PMCID: PMC6851497

122. Shrestha R, Fajardo E, Gil N, Fidelis K, Kryshtafovych A, Monastyrskyy B, Fiser A
Assessing the accuracy of contact predictions in CASP13.
Proteins (2019) 87(12) : 1058-1068
PMID: 31587357     PMCID: PMC6851495

121. Viswanathan R, Fajardo E, Steinberg G, Haller M, Fiser A
Protein-protein binding supersites.
PLoS Comput Biol (2019) 15(1) : e1006704
PMID: 30615604     PMCID: PMC6336348

120. Zepecki JP, Snyder KM, Moreno MM, Fajardo E, Fiser A, Ness J, Sarkar A, Toms SA, Tapinos N
Regulation of human glioma cell migration, tumor growth, and stemness gene expression using a Lck targeted inhibitor.
Oncogene (2019) 38(10) : 1734-1750
PMID: 30353164     PMCID: PMC6462869

119. Aluri S, Zhao R, Lin K, Shin DS, Fiser A, Goldman ID
Substitutions that lock and unlock the proton-coupled folate transporter (PCFT-SLC46A1) in an inward-open conformation.
J Biol Chem (2019) 294(18) : 7245-7258
PMID: 30858177     PMCID: PMC6509503

118. Shrestha R, Garrett SC, Almo SC, Fiser A
Computational Redesign of PD-1 Interface for PD-L1 Ligand Selectivity.
Structure (2019) 27(5) : 829-836.e3
PMID: 30930066     PMCID: PMC6745709

117. Ajasin DO, Rao VR, Wu X, Ramasamy S, Pujato M, Ruiz AP, Fiser A, Bresnick AR, Kalpana GV, Prasad VR
CCL2 mobilizes ALIX to facilitate Gag-p6 mediated HIV-1 virion release.
Elife (2019) 8,
PMID: 31172941     PMCID: PMC6592687

116. Gil N, Fiser A
The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis.
Bioinformatics (2019) 35(1) : 12-19
PMID: 29947739     PMCID: PMC6298051

115. Aluri S, Zhao R, Fiser A, Goldman ID
Substituted-cysteine accessibility and cross-linking identify an exofacial cleft in the 7th and 8th helices of the proton-coupled folate transporter (SLC46A1).
Am J Physiol Cell Physiol (2018) 314(3) : C289-C296
PMID: 29167151     PMCID:

114. Aluri S, AUID- ORCID: 0000-0003-4084-1747, Zhao R, Lubout C, Goorden SMI, Fiser A, Goldman ID
Hereditary folate malabsorption due to a mutation in the external gate of the proton-coupled folate transporter SLC46A1.
Blood Adv (2018) 2(1) : 61-68
PMID: 29344585     PMCID: PMC5761628

113. Ducati RG, Namanja-Magliano HA, Harijan RK, Fajardo JE, Fiser A, Daily JP, Schramm VL
Genetic resistance to purine nucleoside phosphorylase inhibition in Plasmodium falciparum.
Proc Natl Acad Sci U S A (2018) 115(9) : 2114-2119
PMID: 29440412     PMCID:

112. Gil N, Fiser A
Identifying Functionally Informative Evolutionary Sequence Profiles.
Bioinformatics (2017) ,
PMID: 29211823     PMCID:

111. Aluri S, Zhao R, Fiser A, Goldman ID
Residues in the eighth transmembrane domain of the proton-coupled folate transporter (SLC46A1) play an important role in defining the aqueous translocation pathway and in folate substrate binding.
Biochim Biophys Acta (2017) 1859(11) : 2193-2202
PMID: 28802835     PMCID: PMC5624325

110. Carvallo L, Lopez L, Fajardo JE, AUID- ORCID: http://orcid.org/0000-0001-9701-8546, Jaureguiberry-Bravo M, Fiser A, Berman JW
HIV-Tat regulates macrophage gene expression in the context of neuroAIDS.
PLoS One (2017) 12(6) : e0179882
PMID: 28640909     PMCID: PMC5481010

109. Najmi M, Zhao R, Fiser A, Goldman ID
Role of the tryptophan residues in proton-coupled folate transporter (PCFT-SLC46A1) function.
Am J Physiol Cell Physiol (2016) 311(1) : C150-7
PMID: 27251438     PMCID:

108. Ness JK, Skiles AA, Yap EH, Fajardo EJ, Fiser A, Tapinos N
Nuc-ErbB3 regulates H3K27me3 levels and HMT activity to establish epigenetic repression during peripheral myelination.
Glia (2016) 64(6) : 977-92
PMID: 27017927     PMCID:

107. Zhao R, Najmi M, Fiser A, Goldman ID
Identification of an Extracellular Gate for the Proton-coupled Folate Transporter (PCFT-SLC46A1) by Cysteine Cross-linking.
J Biol Chem (2016) 291(15) : 8162-72
PMID: 26884338     PMCID: PMC4825018

106. Yang CH, Yap EH, Xiao H, Fiser A, Horwitz SB
2-(m-Azidobenzoyl)taxol binds differentially to distinct beta-tubulin isotypes.
Proc Natl Acad Sci U S A (2016) 113(40) : 11294-11299
PMID: 27651486     PMCID: PMC5056068

105. Dybas JM, Fiser A
Development of a motif-based topology-independent structure comparison method to identify evolutionarily related folds.
Proteins (2016) 84(12) : 1859-1874
PMID: 27671894     PMCID: PMC5118133

104. Cao LL, Riascos-Bernal DF, Chinnasamy P, Dunaway CM, Hou R, Pujato MA, O'Rourke BP, Miskolci V, Guo L, Hodgson L, Fiser A, Sibinga NE
Control of mitochondrial function and cell growth by the atypical cadherin Fat1.
Nature (2016) 539(7630) : 575-578
PMID: 27828948     PMCID: PMC5257202

103. Yap EH, Fiser A
ProtLID, a Residue-Based Pharmacophore Approach to Identify Cognate Protein Ligands in the Immunoglobulin Superfamily.
Structure (2016) 24(12) : 2217-2226
PMID: 27889206     PMCID:

102. Vallat B, Madrid-Aliste C, Fiser A
Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures.
PLoS Comput Biol (2015) 11(8) : e1004419
PMID: 26252221     PMCID: PMC4529212

101. Carvallo L, Lopez L, Che FY, Lim J, Eugenin EA, Williams DW, Nieves E, Calderon TM, Madrid-Aliste C, Fiser A, Weiss L, Angeletti RH, Berman JW
Buprenorphine decreases the CCL2-mediated chemotactic response of monocytes.
J Immunol (2015) 194(7) : 3246-58
PMID: 25716997     PMCID: PMC4369415

100. Janakiram M, Chinai JM, Fineberg S, Fiser A, Montagna C, Medavarapu R, Castano E, Jeon H, Ohaegbulam KC, Zhao R, Zhao A, Almo SC, Sparano JA, Zang X
Expression, Clinical Significance, and Receptor Identification of the Newest B7 Family Member HHLA2 Protein.
Clin Cancer Res (2015) 21(10) : 2359-66
PMID: 25549724     PMCID: PMC4433806

99. Visentin M, Unal ES, Najmi M, Fiser A, Zhao R, Goldman ID
Identification of Tyr residues that enhance folate substrate binding and constrain oscillation of the proton-coupled folate transporter (PCFT-SLC46A1).
Am J Physiol Cell Physiol (2015) 308(8) : C631-41
PMID: 25608532     PMCID: PMC4398847

98. Yap EH, Rosche T, Almo S, Fiser A
Functional clustering of immunoglobulin superfamily proteins with protein-protein interaction information calibrated hidden markov model sequence profiles.
J Mol Biol (2014) 426(4) : 945-61
PMID: 24246499     PMCID:

97. Xie Q, Ung D, Khafizov K, Fiser A, Cvekl A
Gene regulation by PAX6: structural-functional correlations of missense mutants and transcriptional control of Trpm3/miR-204.
Mol Vis (2014) 20, 270-82
PMID: 24623969     PMCID: PMC3945805

96. Khafizov K, Madrid-Aliste C, Almo SC, Fiser A
Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative.
Proc Natl Acad Sci U S A (2014) 111(10) : 3733-8
PMID: 24567391     PMCID: PMC3956173

95. Tudos E, Meszaros B, Fiser A, Simon I
A word of caution about biological inference - Revisiting cysteine covalent state predictions.
FEBS Open Bio (2014) 4, 310-4
PMID: 24918043     PMCID: PMC4048844

94. Pujato M, Kieken F, Skiles AA, Tapinos N, Fiser A
Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes.
Nucleic Acids Res (2014) 42(22) : 13500-12
PMID: 25428367     PMCID: PMC4267649

93. Fernandez-Fuentes N, Fiser A
A modular perspective of protein structures: application to fragment based loop modeling.
Methods Mol Biol (2013) 932, 141-58
PMID: 22987351     PMCID: PMC3635063

92. Pujato M, MacCarthy T, Fiser A, Bergman A
The underlying molecular and network level mechanisms in the evolution of robustness in gene regulatory networks.
PLoS Comput Biol (2013) 9(1) : e1002865
PMID: 23300434     PMCID: PMC3536627

91. Fajardo JE, Fiser A
Protein structure based prediction of catalytic residues.
BMC Bioinformatics (2013) 14, 63
PMID: 23433045     PMCID: PMC3598644

90. Soniat M, Sampathkumar P, Collett G, Gizzi AS, Banu RN, Bhosle RC, Chamala S, Chowdhury S, Fiser A, Glenn AS, Hammonds J, Hillerich B, Khafizov K, Love JD, Matikainen B, Seidel RD, Toro R, Rajesh Kumar P, Bonanno JB, Chook YM, Almo SC
Crystal structure of human Karyopherin beta2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2.
J Struct Funct Genomics (2013) 14(2) : 31-5
PMID: 23535894     PMCID: PMC3681870

89. Shin DS, Zhao R, Fiser A, Goldman ID
Role of the fourth transmembrane domain in proton-coupled folate transporter function as assessed by the substituted cysteine accessibility method.
Am J Physiol Cell Physiol (2013) 304(12) : C1159-67
PMID: 23552283     PMCID: PMC3680650

88. Rubinstein R, Ramagopal UA, Nathenson SG, Almo SC, Fiser A
Functional classification of immune regulatory proteins.
Structure (2013) 21(5) : 766-76
PMID: 23583034     PMCID: PMC3654037

87. Menon V, Vallat BK, Dybas JM, Fiser A
Modeling proteins using a super-secondary structure library and NMR chemical shift information.
Structure (2013) 21(6) : 891-9
PMID: 23685209     PMCID: PMC3703203

86. Shin DS, Zhao R, Yap EH, Fiser A, Goldman ID
A P425R mutation of the proton-coupled folate transporter causing hereditary folate malabsorption produces a highly selective alteration in folate binding.
Am J Physiol Cell Physiol (2012) ,
PMID: 22345511     PMCID: PMC3361945

85. Lakshmanan V, Rhee K, Wang W, Yu Y, Khafizov K, Fiser A, Wu P, Ndir O, Mboup S, Ndiaye D, Daily J
Metabolomic analysis of patient plasma yields evidence of plant-like alpha-linolenic acid metabolism in Plasmodium falciparum.
J Infect Dis (2012) ,
PMID: 22566569     PMCID: PMC3490690

84. Zhao R, Shin DS, Fiser A, Goldman ID
Identification of a functionally critical GXXG motif and its relationship to the folate binding site of the proton-coupled folate transporter (PCFT-SLC46A1).
Am J Physiol Cell Physiol (2012) 303(6) : C673-81
PMID: 22785121     PMCID: PMC3468349

83. Shin DS, Zhao R, Fiser A, Goldman DI
Functional roles of the A335 and G338 residues of the proton-coupled folate transporter (PCFT-SLC46A1) mutated in hereditary folate malabsorption.
Am J Physiol Cell Physiol (2012) 303(8) : C834-42
PMID: 22843796     PMCID: PMC3469714

82. Che FY, Madrid-Aliste C, Burd B, Zhang H, Nieves E, Kim K, Fiser A, Angeletti RH, Weiss LM
Comprehensive proteomic analysis of membrane proteins in Toxoplasma gondii.
Mol Cell Proteomics (2011) 10(1) : M110.000745
PMID: 20935347     PMCID: PMC3013445

81. Khrapunovich-Baine M, Menon V, Huang Yang CP, Northcote PT, Miller JH, Hogue Angeletti R, Fiser A, Horwitz SB, Xiao H
Hallmarks of molecular action of microtubule stabilizing agents: Effects of epothilone B, ixabepilone, peloruside A, and laulimalide on microtubule conformation.
J Biol Chem (2011) ,
PMID: 21245138     PMCID: PMC3064228

80. Adilakshmi T, Ness-Myers J, Madrid-Aliste C, Fiser A, Tapinos N
A Nuclear Variant of ErbB3 Receptor Tyrosine Kinase Regulates Ezrin Distribution and Schwann Cell Myelination.
J Neurosci (2011) 31(13) : 5106-19
PMID: 21451047     PMCID: PMC3086203

79. Wang L, Rubinstein R, Lines JL, Wasiuk A, Ahonen C, Guo Y, Lu LF, Gondek D, Wang Y, Fava RA, Fiser A, Almo S, Noelle RJ
VISTA, a novel mouse Ig superfamily ligand that negatively regulates T cell responses.
J Exp Med (2011) 208(3) : 577-92
PMID: 21383057     PMCID: PMC3058578

78. Lim J, Menon V, Bitzer M, Miller LM, Madrid-Aliste C, Weiss LM, Fiser A, Angeletti RH
Frozen tissue can provide reproducible proteomic results of subcellular fractionation.
Anal Biochem (2011) ,
PMID: 21802400     PMCID: PMC3164751

77. Yan F, Che FY, Nieves E, Weiss LM, Angeletti RH, Fiser A
Photo-assisted peptide enrichment in protein complex cross-linking analysis of a model homodimeric protein using mass spectrometry.
Proteomics (2011) 11(20) : 4109-15
PMID: 21834138     PMCID: PMC3465073

76. Xiao H, El Bissati K, Verdier-Pinard P, Burd B, Zhang H, Kim K, Fiser A, Angeletti RH, Weiss LM
Post-translational modifications to Toxoplasma gondii alpha- and beta-tubulins include novel C-terminal methylation.
J Proteome Res (2010) 9(1) : 359-72
PMID: 19886702     PMCID: PMC2813730

75. Rykunov D, Fiser A
New statistical potential for quality assessment of protein models and a survey of energy functions.
BMC Bioinformatics (2010) 11, 128
PMID: 20226048     PMCID: PMC2853469

74. Fernandez-Fuentes N, Dybas JM, Fiser A
Structural characteristics of novel protein folds.
PLoS Comput Biol (2010) 6(4) : e1000750
PMID: 20421995     PMCID: PMC2858679

73. Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, Chance MR, Baker D, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Sali A, Sauder JM, Burley SK
Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution.
Proteins (2010) 78(14) : 3056-62
PMID: 20737437     PMCID: PMC2989796

72. Shin DS, Min SH, Russell L, Zhao R, Fiser A, Goldman ID
Functional roles of aspartate residues of the human proton-coupled folate transporter (PCFT; SLC46A1); D156, mutated in hereditary folate malabsorption, is critical for protein stability; D109 is irreplaceable.
Blood (2010) ,
PMID: 20805364     PMCID: PMC3012536

71. Fiser A
Template-based protein structure modeling.
Methods Mol Biol (2010) 673, 73-94
PMID: 20835794     PMCID:

70. Dbouk HA, Pang H, Fiser A, Backer JM
A biochemical mechanism for the oncogenic potential of the p110beta catalytic subunit of phosphoinositide 3-kinase.
Proc Natl Acad Sci U S A (2010) 107(46) : 19897-902
PMID: 21030680     PMCID: PMC2993364

69. Rykunov D, Steinberger E, Madrid-Aliste CJ, Fiser A
Improved scoring function for comparative modeling using the M4T method.
J Struct Funct Genomics (2009) 10(1) : 95-9
PMID: 18985440     PMCID:

68. Madrid-Aliste CJ, Dybas JM, Hogue Angeletti R, Weiss LM, Kim K, Simon I, Fiser A
EPIC-DB: a proteomics database for studying Apicomplexan organisms.
BMC Genomics (2009) 10(1) : 38
PMID: 19159464     PMCID: PMC2652494

67. Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL Jr, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR Jr, Kortemme T, Kryshtafovych A, Montelione GT,
Outcome of a workshop on applications of protein models in biomedical research.
Structure (2009) 17(2) : 151-9
PMID: 19217386     PMCID: PMC2739730

66. Nair R, Liu J, Soong TT, Acton TB, Everett JK, Kouranov A, Fiser A, Godzik A, Jaroszewski L, Orengo C, Montelione GT, Rost B
Structural genomics is the largest contributor of novel structural leverage.
J Struct Funct Genomics (2009) 10(2) : 181-91
PMID: 19194785     PMCID: PMC2705706

65. Blakaj DM, Fernandez-Fuentes N, Chen Z, Hegde R, Fiser A, Burk RD, Brenowitz M
Evolutionary and biophysical relationships among the papillomavirus E2 proteins.
Front Biosci (2009) 14, 900-17
PMID: 19273107     PMCID: PMC3705561

64. Unal ES, Zhao R, Chang MH, Fiser A, Romero MF, Goldman ID
The functional roles of the His247 and His281 residues in folate and proton translocation mediated by the human proton-coupled folate transporter (PCFT-SLC46A1).
J Biol Chem (2009) 284(26) : 17846-57
PMID: 19389703     PMCID: PMC2719423

63. Weiss LM, Fiser A, Angeletti RH, Kim K
Toxoplasma gondii proteomics.
Expert Rev Proteomics (2009) 6(3) : 303-13
PMID: 19489701     PMCID: PMC2741161

62. Dessailly BH, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, Lee D, Fiser A, Godzik A, Rost B, Orengo C
PSI-2: Structural Genomics to Cover Protein Domain Family Space.
Structure (2009) 17(6) : 869-81
PMID: 19523904     PMCID: PMC2920419

61. Abboud N, De Jesus M, Nakouzi A, Cordero RJ, Pujato M, Fiser A, Rivera J, Casadevall A
Identification of linear epitopes in bacillus anthracis protective antigen bound by neutralizing antibodies.
J Biol Chem (2009) 284(37) : 25077-86
PMID: 19617628     PMCID: PMC2757211

60. Yan F, Che FY, Rykunov D, Nieves E, Fiser A, Weiss LM, Hogue Angeletti R
Nonprotein Based Enrichment Method to Analyze Peptide Cross-Linking in Protein Complexes.
Anal Chem (2009) 81(17) : 7149-59
PMID: 19642656     PMCID: PMC2765915

59. Grozdanov PN, Fernandez-Fuentes N, Fiser A, Meier UT
Pathogenic NAP57 mutations decrease ribonucleoprotein assembly in dyskeratosis congenita.
Hum Mol Genet (2009) 18(23) : 4546-51
PMID: 19734544     PMCID: PMC2773269

58. Trofa D, Agovino M, Stehr F, Schafer W, Rykunov D, Fiser A, Hamari Z, Nosanchuk JD, Gacser A
Acetylsalicylic acid (aspirin) reduces damage to reconstituted human tissues infected with Candida species by inhibiting extracellular fungal lipases.
Microbes Infect (2009) 11(14-15) : 1131-9
PMID: 19703582     PMCID: PMC2787780

57. Khrapunovich-Baine M, Menon V, Verdier-Pinard P, Smith AB 3rd, Angeletti RH, Fiser A, Horwitz SB, Xiao H
Distinct pose of discodermolide in taxol binding pocket drives a complementary mode of microtubule stabilization.
Biochemistry (2009) 48(49) : 11664-77
PMID: 19863156     PMCID: PMC2845443

56. Graslund S, Nordlund P, Weigelt J, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo
Protein production and purification.
Nat Methods (2008) 5(2) : 135-46
PMID: 18235434     PMCID: PMC3178102

55. Rubinstein R, Fiser A
Predicting disulfide bond connectivity in proteins by correlated mutations analysis.
Bioinformatics (2008) 24(4) : 498-504
PMID: 18203772     PMCID:

54. Dybas JM, Madrid-Aliste CJ, Che FY, Nieves E, Rykunov D, Angeletti RH, Weiss LM, Kim K, Fiser A
Computational Analysis and Experimental Validation of Gene Predictions in Toxoplasma gondii.
PLoS ONE (2008) 3(12) : e3899
PMID: 19065262     PMCID: PMC2587701

53. Graslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, H
Protein production and purification.
Nat Methods (2008) 5(2) : 135-46
PMID: 18235434     PMCID: PMC3178102

52. Torres M, Fernandez-Fuentes N, Fiser A, Casadevall A
Exchanging murine and human immunoglobulin constant chains affects the kinetics and thermodynamics of antigen binding and chimeric antibody autoreactivity.
PLoS ONE (2007) 2(12) : e1310
PMID: 18074033     PMCID: PMC2110899

51. Almo SC, Bonanno JB, Sauder JM, Emtage S, Dilorenzo TP, Malashkevich V, Wasserman SR, Swaminathan S, Eswaramoorthy S, Agarwal R, Kumaran D, Madegowda M, Ragumani S, Patskovsky Y, Alvarado J, Ramagopal UA, Faber-Barata J, Chance MR, Sali A, Fiser A, Zhang
Structural genomics of protein phosphatases.
J Struct Funct Genomics (2007) 8(2-3) : 121-40
PMID: 18058037     PMCID:

50. Fernandez-Fuentes N, Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments.
Bioinformatics (2007) 23(19) : 2558-65
PMID: 17823132     PMCID:

49. Feyfant E, Sali A, Fiser A
Modeling mutations in protein structures.
Protein Sci (2007) 16(9) : 2030-41
PMID: 17766392     PMCID: PMC2206969

48. Fernandez-Fuentes N, Madrid-Aliste CJ, Rai BK, Fajardo JE, Fiser A
M4T: a comparative protein structure modeling server.
Nucleic Acids Res (2007) 35(Web S) : W363-8
PMID: 17517764     PMCID: PMC1933164

47. Torres M, Fernandez-Fuentes N, Fiser A, Casadevall A
The immunoglobulin heavy chain constant region affects kinetic and thermodynamic parameters of antibody variable region interactions with antigen.
J Biol Chem (2007) 282(18) : 13917-27
PMID: 17353196     PMCID:

46. Rykunov D, Fiser A
Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials.
Proteins (2007) 67(3) : 559-68
PMID: 17335003     PMCID:

45. Manjasetty BA, Shi W, Zhan C, Fiser A, Chance MR
A high-throughput approach to protein structure analysis.
Genet Eng (N Y) (2007) 28, 105-28
PMID: 17153936     PMCID:

44. Vetting MW, Hegde SS, Fajardo JE, Fiser A, Roderick SL, Takiff HE, Blanchard JS
Pentapeptide repeat proteins.
Biochemistry (2006) 45(1) : 1-10
PMID: 16388575     PMCID: PMC2566302

43. Rai BK, Fiser A
Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling.
Proteins (2006) 63(3) : 644-61
PMID: 16437570     PMCID:

42. Fernandez-Fuentes N, Oliva B, Fiser A
A supersecondary structure library and search algorithm for modeling loops in protein structures.
Nucleic Acids Res (2006) 34(7) : 2085-97
PMID: 16617149     PMCID: PMC1440879

41. Xiao H, Verdier-Pinard P, Fernandez-Fuentes N, Burd B, Angeletti R, Fiser A, Horwitz SB, Orr GA
Insights into the mechanism of microtubule stabilization by Taxol.
Proc Natl Acad Sci U S A (2006) 103(27) : 10166-73
PMID: 16801540     PMCID: PMC1502429

40. Fernandez-Fuentes N, Fiser A
Saturating representation of loop conformational fragments in structure databanks.
BMC Struct Biol (2006) 6, 15
PMID: 16820050     PMCID: PMC1574324

39. Fernandez-Fuentes N, Zhai J, Fiser A
ArchPRED: a template based loop structure prediction server.
Nucleic Acids Res (2006) 34(Web S) : W173-6
PMID: 16844985     PMCID: PMC1538831

38. Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A
MMM: a sequence-to-structure alignment protocol.
Bioinformatics (2006) 22(21) : 2691-2
PMID: 16928737     PMCID:

37. Chattopadhyay K, Bhatia S, Fiser A, Almo SC, Nathenson SG
Structural basis of inducible costimulator ligand costimulatory function: determination of the cell surface oligomeric state and functional mapping of the receptor binding site of the protein.
J Immunol (2006) 177(6) : 3920-9
PMID: 16951355     PMCID:

36. Reichman C, Singh K, Liu Y, Singh S, Li H, Fajardo JE, Fiser A, Birge RB
Transactivation of Abl by the Crk II adapter protein requires a PNAY sequence in the Crk C-terminal SH3 domain.
Oncogene (2005) 24(55) : 8187-99
PMID: 16158059     PMCID:

35. Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR, Emtage S, D'Amico KL, Burley SK
New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative.
J Struct Funct Genomics (2005) 6(2-3) : 225-32
PMID: 16211523     PMCID:

34. Zhan C, Fedorov EV, Shi W, Ramagopal UA, Thirumuruhan R, Manjasetty BA, Almo SC, Fiser A, Chance MR, Fedorov AA
The ybeY protein from Escherichia coli is a metalloprotein.
Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 61(Pt 11) : 959-63
PMID: 16511207     PMCID: PMC1978141

33. Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A
MODBASE, a database of annotated comparative protein structure models, and associated resources.
Nucleic Acids Res (2004) 32(Datab) : D217-22
PMID: 14681398     PMCID: PMC308829

32. Tudos E, Fiser A, Simon A, Dosztanyi Z, Fuxreiter M, Magyar C, Simon I
Noncovalent cross-links in context with other structural and functional elements of proteins.
J Chem Inf Comput Sci (2004) 44(2) : 347-51
PMID: 15032510     PMCID:

31. Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N
High-throughput computational and experimental techniques in structural genomics.
Genome Res (2004) 14(10B) : 2145-54
PMID: 15489337     PMCID: PMC528931

30. Fiser A
Protein structure modeling in the proteomics era.
Expert Rev Proteomics (2004) 1(1) : 97-110
PMID: 15966803     PMCID:

29. Lee SA, Shen EL, Fiser A, Sali A, Guo S
The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons.
Development (2003) 130(12) : 2669-79
PMID: 12736211     PMCID:

28. Dosztanyi Z, Magyar C, Tusnady GE, Cserzo M, Fiser A, Simon I
Servers for sequence-structure relationship analysis and prediction.
Nucleic Acids Res (2003) 31(13) : 3359-63
PMID: 12824327     PMCID: PMC168995

27. Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A
Tools for comparative protein structure modeling and analysis.
Nucleic Acids Res (2003) 31(13) : 3375-80
PMID: 12824331     PMCID: PMC168950

26. Hargitai J, Lewis H, Boros I, Racz T, Fiser A, Kurucz I, Benjamin I, Vigh L, Penzes Z, Csermely P, Latchman DS
Bimoclomol, a heat shock protein co-inducer, acts by the prolonged activation of heat shock factor-1.
Biochem Biophys Res Commun (2003) 307(3) : 689-95
PMID: 12893279     PMCID:

25. Fiser A, Sali A
ModLoop: automated modeling of loops in protein structures.
Bioinformatics (2003) 19(18) : 2500-1
PMID: 14668246     PMCID:

24. Fiser A, Sali A
Modeller: generation and refinement of homology-based protein structure models.
Methods Enzymol (2003) 374, 461-91
PMID: 14696385     PMCID:

23. Fiser, A. and Sali, A
Comparative protein structure modeling
Protein Structure: Determination, Analysis, and Application for Drug discovery. Marcel Dekker, New York, (2003) , pp 167-206
PMID: 0     PMCID:

22. Marti-Renom MA., Fiser A., Madhusudhan M.S., John B., Stuart A., Eswar N., Pieper U., Shen, M-Y. and Sali, A.
Modeling protein structure from its sequence
Current Protocols in Bioinformatics John Wiley and Sons, Inc. V. 5 (2003) , pp. 5.1.1.-5.1.32
PMID: 0     PMCID:

21. Fiser A, Filipe SR, Tomasz A
Cell wall branches, penicillin resistance and the secrets of the MurM protein.
Trends Microbiol (2003) 11(12) : 547-53
PMID: 14659686     PMCID:

20. Fiser A, Simon I
Predicting redox state of cysteines in proteins.
Methods Enzymol (2002) 353, 10-21
PMID: 12078485     PMCID:

19. Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A
Reliability of assessment of protein structure prediction methods.
Structure (2002) 10(3) : 435-40
PMID: 12005441     PMCID:

18. Fiser A, Feig M, Brooks CL 3rd, Sali A
Evolution and physics in comparative protein structure modeling.
Acc Chem Res (2002) 35(6) : 413-21
PMID: 12069626     PMCID:

17. Vernal J, Fiser A, Sali A, Muller M, Cazzulo JJ, Nowicki C
Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis.
Biochem Biophys Res Commun (2002) 293(1) : 633-9
PMID: 12054650     PMCID:

16. A. Fiser, R. Sánchez, F. Melo and A. Sali.
Comparative protein structure modeling in Computational Biochemistry and Biophysics
Marcel Dekker. M. Watanabe, B. Roux, A. MacKerell, and O. Becker, editors (2001) , 275-312
PMID: 0     PMCID:

15. Barrientos LG, Campos-Olivas R, Louis JM, Fiser A, Sali A, Gronenborn AM
1H, 13C, 15N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N.
J Biomol NMR (2001) 19(3) : 289-90
PMID: 11330821     PMCID:

14. Simon I, Fiser A, Tusnady GE
Predicting protein conformation by statistical methods.
Biochim Biophys Acta (2001) 1549(2) : 123-36
PMID: 11690649     PMCID:

13. Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Fiser A, Pazos F, Valencia A, Sali A, Rost B
EVA: continuous automatic evaluation of protein structure prediction servers.
Bioinformatics (2001) 17(12) : 1242-3
PMID: 11751240     PMCID:

12. Fiser A, Simon I
Predicting the oxidation state of cysteines by multiple sequence alignment.
Bioinformatics (2000) 16(3) : 251-6
PMID: 10869018     PMCID:

11. Wu G, McArthur AG, Fiser A, Sali A, Sogin ML, Mllerm M
Core histones of the amitochondriate protist, Giardia lamblia.
Mol Biol Evol (2000) 17(8) : 1156-63
PMID: 10908635     PMCID:

10. Fiser A, Do RK, Sali A
Modeling of loops in protein structures.
Protein Sci (2000) 9(9) : 1753-73
PMID: 11045621     PMCID: PMC2144714

9. Fiser A, Vertessy BG
Altered subunit communication in subfamilies of trimeric dUTPases.
Biochem Biophys Res Commun (2000) 279(2) : 534-42
PMID: 11118321     PMCID:

8. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A
Comparative protein structure modeling of genes and genomes.
Annu Rev Biophys Biomol Struct (2000) 29, 291-325
PMID: 10940251     PMCID:

7. Wu G, Fiser A, ter Kuile B, Sali A, Muller M
Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase.
Proc Natl Acad Sci U S A (1999) 96(11) : 6285-90
PMID: 10339579     PMCID: PMC26873

6. Fiser A, Dosztanyi Z, Simon I
The role of long-range interactions in defining the secondary structure of proteins is overestimated.
Comput Appl Biosci (1997) 13(3) : 297-301
PMID: 9183535     PMCID:

5. Dosztanyi Z, Fiser A, Simon I
Stabilization centers in proteins: identification, characterization and predictions.
J Mol Biol (1997) 272(4) : 597-612
PMID: 9325115     PMCID:

4. Fiser A, Simon I, Barton GJ
Conservation of amino acids in multiple alignments: aspartic acid has unexpected conservation.
FEBS Lett (1996) 397(2-3) : 225-9
PMID: 8955352     PMCID:

3. Tudos E, Fiser A, Simon I
Different sequence environments of amino acid residues involved and not involved in long-range interactions in proteins.
Int J Pept Protein Res (1994) 43(2) : 205-8
PMID: 8200741     PMCID:

2. Fiser A, Tusnady GE, Simon I
Chaos game representation of protein structures.
J Mol Graph (1994) 12(4) : 302-4, 295
PMID: 7696222     PMCID:

1. Fiser A, Cserzo M, Tudos E, Simon I
Different sequence environments of cysteines and half cystines in proteins. Application to predict disulfide forming residues.
FEBS Lett (1992) 302(2) : 117-20
PMID: 1633841     PMCID: