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Andras Fiser
Department of Biochemistry and Center for Bioinformatics, Albert Einstein College of Medicine, New York, United States of America

Faculty Member: Structural Biology > Structural Genomics [ since 6 November 2002 ]
[ Homepage ] [ Evaluations ]
Home page

http://www.fiserlab.org

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Evaluations

Fast screening of protein surfaces using geometric invariant fingerprints.
Yin S, Proctor EA, Lugovskoy AA, Dokholyan NV
Proc Natl Acad Sci U S A 2009 Sep 29 106(39):16622-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 5 Mar 2010

Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.
Pascual-García A, Abia D, Ortiz AR, Bastolla U
PLoS Comput Biol 2009 Mar 5:e1000331 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 29 Sep 2009

Analysis of combinatorial cis-regulation in synthetic and genomic promoters.
Gertz J, Siggia ED, Cohen BA
Nature 2009 Jan 8 457(7226):215-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Mario Pujato and Andras Fiser
Evaluated 12 Aug 2009

The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world.
Wang M, Caetano-Anollés G
Structure 2009 Jan 17(1):66-78 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Mario Pujato and Andras Fiser
Evaluated 18 Feb 2009

NMR structures of two designed proteins with high sequence identity but different fold and function.
He Y, Chen Y, …, Bryan PN, Orban J
Proc Natl Acad Sci U S A 2008 Sep 23 105(38):14412-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Gira Bhabha and H Jane Dyson / Mario Pujato and Andras Fiser / Nick Grishin
Evaluated 2 Jan 2009

Exalign: a new method for comparative analysis of exon-intron gene structures.
Pavesi G, Zambelli F, Caggese C, Pesole G
Nucleic Acids Res 2008 May 36(8):e47 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 28 Oct 2008

Binding-induced folding of a natively unstructured transcription factor.
Turjanski AG, Gutkind JS, Best RB, Hummer G
PLoS Comput Biol 2008 Apr 4(4):e1000060 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 19 May 2008

Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
Trabuco LG, Villa E, …, Frank J, Schulten K
Structure 2008 May 16(5):673-83 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 13 May 2008

How protein stability and new functions trade off.
Tokuriki N, Stricher F, Serrano L, Tawfik DS
PLoS Comput Biol 2008 Feb 4(2):e1000002 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 13 May 2008

Topology independent protein structural alignment.
Dundas J, Binkowski TA, DasGupta B, Liang J
BMC Bioinformatics 2007 8:388 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 16 Jan 2008

Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back.
Chen J, Dima RI, Thirumalai D
J Mol Biol 2007 Nov 16 374(1):250-66 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 29 Oct 2007

Connecting protein structure with predictions of regulatory sites.
Morozov AV, Siggia ED
Proc Natl Acad Sci U S A 2007 Apr 24 104(17):7068-73 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser / Gabriele Varani
Evaluated 1 May 2007

Statistical and conformational analysis of the electron density of protein side chains.
Shapovalov MV, Dunbrack RL
Proteins 2007 Feb 1 66(2):279-303 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 5 Jan 2007

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.
Li W, Godzik A
Bioinformatics 2006 Jul 1 22(13):1658-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 27 Jul 2006

A limited universe of membrane protein families and folds.
Oberai A, Ihm Y, Kim S, Bowie JU
Protein Sci 2006 Jul 15(7):1723-34 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 27 Jul 2006

Role of disulfide bonds in modulating internal motions of proteins to tune their function: molecular dynamics simulation of scorpion toxin Lqh III.
Moghaddam ME, Naderi-Manesh H
Proteins 2006 Apr 1 63(1):188-96 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 21 Apr 2006

Physical origins of protein superfamilies.
Zeldovich KB, Berezovsky IN, Shakhnovich EI
J Mol Biol 2006 Apr 7 357(4):1335-43 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 18 Apr 2006

Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions.
Huang YM, Bystroff C
Bioinformatics 2006 Feb 15 22(4):413-22 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 20 Feb 2006

Using information theory to search for co-evolving residues in proteins.
Martin LC, Gloor GB, Dunn SD, Wahl LM
Bioinformatics 2005 Nov 15 21(22):4116-24 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 5 Dec 2005

Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design.
Cheng G, Qian B, Samudrala R, Baker D
Nucleic Acids Res 2005 33(18):5861-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 2 Dec 2005

Protein flexibility and rigidity predicted from sequence.
Schlessinger A, Rost B
Proteins 2005 Oct 1 61(1):115-26 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 1 Sep 2005

Do all backbone polar groups in proteins form hydrogen bonds?
Fleming PJ, Rose GD
Protein Sci 2005 Jul 14(7):1911-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 30 Aug 2005

Multiple flexible structure alignment using partial order graphs.
Ye Y, Godzik A
Bioinformatics 2005 May 15 21(10):2362-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 27 Jun 2005

Protein sequence randomization: efficient estimation of protein stability using knowledge-based potentials.
Wiederstein M, Sippl MJ
J Mol Biol 2005 Feb 4 345(5):1199-212 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 29 Mar 2005

Identification of the ligand binding sites on the molecular surface of proteins.
Kinoshita K, Nakamura H
Protein Sci 2005 Mar 14(3):711-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 17 Mar 2005

A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins.
Linding R, Schymkowitz J, …, Diella F, Serrano L
J Mol Biol 2004 Sep 3 342(1):345-53 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 16 Mar 2005

Inter-residue distances derived from fold contact propensities correlate with evolutionary substitution costs.
Williams G, Doherty P
BMC Bioinformatics 2004 Oct 18 5:153 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 13 Dec 2004

Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation.
Qian B, Ortiz AR, Baker D
Proc Natl Acad Sci U S A 2004 Oct 26 101(43):15346-51 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Matthew Jacobson / Andras Fiser
Evaluated 10 Dec 2004

Improving fold recognition without folds.
Przybylski D, Rost B
J Mol Biol 2004 Jul 30 341(1):255-69 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 19 Aug 2004

A structural pattern-based method for protein fold recognition.
Taylor WR, Jonassen I
Proteins 2004 Aug 1 56(2):222-34 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 13 Aug 2004

Influence of conservation on calculations of amino acid covariance in multiple sequence alignments.
Fodor AA, Aldrich RW
Proteins 2004 Aug 1 56(2):211-21 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 10 Aug 2004

Why are both ends of the polypeptide chain on the outside of proteins?
Hovmöller S, Zhou T
Proteins 2004 May 1 55(2):219-22 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 5 Aug 2004

Flexible structure alignment by chaining aligned fragment pairs allowing twists.
Ye Y, Godzik A
Bioinformatics 2003 Oct 19 Suppl 2:ii246-55 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 14 May 2004

A combined transmembrane topology and signal peptide prediction method.
Käll L, Krogh A, Sonnhammer EL
J Mol Biol 2004 May 14 338(5):1027-36 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 13 May 2004

The PDB is a covering set of small protein structures.
Kihara D, Skolnick J
J Mol Biol 2003 Dec 5 334(4):793-802 [abstract on PubMed] [related articles] [order article]
Selected by | Andras Fiser
Evaluated 3 Mar 2004

From analysis of protein structural alignments toward a novel approach to align protein sequences.
Sunyaev SR, Bogopolsky GA, …, Finkelstein AV, Roytberg MA
Proteins 2004 Feb 15 54(3):569-82 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser
Evaluated 1 Mar 2004

Analysing six types of protein-protein interfaces.
Ofran Y, Rost B
J Mol Biol 2003 Jan 10 325(2):377-87 [abstract on PubMed] [related articles] [order article]
Selected by | Rebecca Wade / Rob Russell / Andras Fiser
Evaluated 23 Dec 2003

In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling.
Contreras-Moreira B, Fitzjohn PW, Bates PA
J Mol Biol 2003 May 2 328(3):593-608 [abstract on PubMed] [related articles] [order article]
Selected by | Andras Fiser
Evaluated 1 Oct 2003

Identification of substrate binding sites in enzymes by computational solvent mapping.
Silberstein M, Dennis S, …, Clodfelter K, Vajda S
J Mol Biol 2003 Oct 3 332(5):1095-113 [abstract on PubMed] [related articles] [order article]
Selected by | Andras Fiser
Evaluated 24 Sep 2003

Triggering loops and enzyme function: identification of loops that trigger and modulate movements.
Gunasekaran K, Ma B, Nussinov R
J Mol Biol 2003 Sep 5 332(1):143-59 [abstract on PubMed] [related articles] [order article]
Selected by | Andras Fiser
Evaluated 8 Sep 2003

SATCHMO: sequence alignment and tree construction using hidden Markov models.
Edgar RC, Sjölander K
Bioinformatics 2003 Jul 22 19(11):1404-11 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 29 Jul 2003

Propensities, probabilities, and the Boltzmann hypothesis.
Shortle D
Protein Sci 2003 Jun 12(6):1298-302 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 28 May 2003

Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation.
Ota M, Kinoshita K, Nishikawa K
J Mol Biol 2003 Apr 11 327(5):1053-64 [abstract on PubMed] [related articles] [order article]
Selected by | Andras Fiser / Janet Thornton
Evaluated 25 Apr 2003

Efficient identification of side-chain patterns using a multidimensional index tree.
Hamelryck T
Proteins 2003 Apr 1 51(1):96-108 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andras Fiser / Janet Thornton
Evaluated 3 Mar 2003

On filtering false positive transmembrane protein predictions.
Cserzö M, Eisenhaber F, Eisenhaber B, Simon I
Protein Eng 2002 Sep 15(9):745-52 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 3 Mar 2003

The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds.
Mallick P, Weiss R, Eisenberg D
Proc Natl Acad Sci U S A 2002 Dec 10 99(25):16041-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser / Janet Thornton
Evaluated 16 Dec 2002

MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison.
Ortiz AR, Strauss CE, Olmea O
Protein Sci 2002 Nov 11(11):2606-21 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Andras Fiser
Evaluated 11 Nov 2002

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