article
review, book chapter
69.
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
68.
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
67.
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
66.
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
65.
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
64.
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
63.
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
62.
Weiss LM, Fiser A, Angeletti RH, Kim K
Toxoplasma gondii proteomics.
Expert Rev Proteomics (2009)
6(3) : 303-13
61.
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
60.
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
59.
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
58.
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
57.
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
56.
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
55.
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
54.
Rubinstein R, Fiser A
Predicting disulfide bond connectivity in proteins by correlated mutations analysis.
Bioinformatics (2008)
24(4) : 498-504
53.
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
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
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
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
49.
Feyfant E, Sali A, Fiser A
Modeling mutations in protein structures.
Protein Sci (2007)
16(9) : 2030-41
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
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
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
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
44.
Vetting MW, Hegde SS, Fajardo JE, Fiser A, Roderick SL, Takiff HE, Blanchard JS
Pentapeptide repeat proteins.
Biochemistry (2006)
45(1) : 1-10
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
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
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
40.
Fernandez-Fuentes N, Fiser A
Saturating representation of loop conformational fragments in structure databanks.
BMC Struct Biol (2006)
6, 15
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
38.
Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A
MMM: a sequence-to-structure alignment protocol.
Bioinformatics (2006)
22(21) : 2691-2
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
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
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
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
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
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
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
30.
Fiser A
Protein structure modeling in the proteomics era.
Expert Rev Proteomics (2004)
1(1) : 97-110
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
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
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
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
25.
Fiser A, Sali A
ModLoop: automated modeling of loops in protein structures.
Bioinformatics (2003)
19(18) : 2500-1
24.
Fiser A, Sali A
Modeller: generation and refinement of homology-based protein structure models.
Methods Enzymol (2003)
374, 461-91
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
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
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
20.
Fiser A, Simon I
Predicting redox state of cysteines in proteins.
Methods Enzymol (2002)
353, 10-21
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
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
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
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
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
14.
Simon I, Fiser A, Tusnady GE
Predicting protein conformation by statistical methods.
Biochim Biophys Acta (2001)
1549(2) : 123-36
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
12.
Fiser A, Simon I
Predicting the oxidation state of cysteines by multiple sequence alignment.
Bioinformatics (2000)
16(3) : 251-6
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
10.
Fiser A, Do RK, Sali A
Modeling of loops in protein structures.
Protein Sci (2000)
9(9) : 1753-73
9.
Fiser A, Vertessy BG
Altered subunit communication in subfamilies of trimeric dUTPases.
Biochem Biophys Res Commun (2000)
279(2) : 534-42
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
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
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
5.
Dosztanyi Z, Fiser A, Simon I
Stabilization centers in proteins: identification, characterization and predictions.
J Mol Biol (1997)
272(4) : 597-612
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
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
2.
Fiser A, Tusnady GE, Simon I
Chaos game representation of protein structures.
J Mol Graph (1994)
12(4) : 302-4, 295
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