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Nick Grishin
Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, United States of America

Faculty Member: Genomics & Genetics > Bioinformatics [ since 1 March 2010 ]
[ Evaluations ]
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Evaluations

A new generation of homology search tools based on probabilistic inference.
Eddy SR
Genome Inform 2009 Oct 23(1):205-11 [abstract on PubMed] [related articles] [order article]
Selected by | Nick Grishin
Evaluated 4 Mar 2010

The continuity of protein structure space is an intrinsic property of proteins.
Skolnick J, Arakaki AK, Lee SY, Brylinski M
Proc Natl Acad Sci U S A 2009 Sep 15 106(37):15690-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin
Evaluated 3 Mar 2010

On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
Mulkidjanian AY, Galperin MY
Biol Direct 2009 4:27 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 2 Mar 2010

A minimal sequence code for switching protein structure and function.
Alexander PA, He Y, …, Orban J, Bryan PN
Proc Natl Acad Sci U S A 2009 Dec 15 106(50):21149-54 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Alina Peterson and Adolfo Garcia-Sastre / Gira Bhabha and H Jane Dyson / Nick Grishin
Evaluated 2 Mar 2010

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 27 Jan 2009

Structure of a site-2 protease family intramembrane metalloprotease.
Feng L, Yan H, …, Jeffrey PD, Shi Y
Science 2007 Dec 7 318(5856):1608-12 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin
Evaluated 25 Feb 2008

Detection of DNA structural motifs in functional genomic elements.
Greenbaum JA, Parker SC, Tullius TD
Genome Res 2007 Jun 17(6):940-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 18 Feb 2008

A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels.
Ammelburg M, Hartmann MD, …, Lupas AN, Coles M
Structure 2007 Dec 15(12):1577-90 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin
Evaluated 18 Feb 2008

The design and characterization of two proteins with 88% sequence identity but different structure and function.
Alexander PA, He Y, …, Orban J, Bryan PN
Proc Natl Acad Sci U S A 2007 Jul 17 104(29):11963-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard / Nick Grishin / Tobin Sosnick
Evaluated 26 Jul 2007

Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution.
Dantas G, Watters AL, …, Varani G, Baker D
J Mol Biol 2006 Oct 6 362(5):1004-24 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin
Evaluated 5 Jan 2007

Introns and the origin of nucleus-cytosol compartmentalization.
Martin W, Koonin EV
Nature 2006 Mar 2 440(7080):41-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin / Marilyn Parsons
Evaluated 13 Mar 2006

Placing confidence limits on the molecular age of the human-chimpanzee divergence.
Kumar S, Filipski A, …, Walker A, Hedges SB
Proc Natl Acad Sci U S A 2005 Dec 27 102(52):18842-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 13 Feb 2006

A simple physical model for scaling in protein-protein interaction networks.
Deeds EJ, Ashenberg O, Shakhnovich EI
Proc Natl Acad Sci U S A 2006 Jan 10 103(2):311-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin / Deyou Zheng
Evaluated 11 Jan 2006

Quasi-consensus-based comparison of profile hidden Markov models for protein sequences.
Kahsay RY, Wang G, …, Liao L, Dunbrack R
Bioinformatics 2005 May 15 21(10):2287-93 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 16 Aug 2005

ProbCons: Probabilistic consistency-based multiple sequence alignment.
Do CB, Mahabhashyam MS, Brudno M, Batzoglou S
Genome Res 2005 Feb 15(2):330-40 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 15 Feb 2005

Recapitulation of protein family divergence using flexible backbone protein design.
Saunders CT, Baker D
J Mol Biol 2005 Feb 18 346(2):631-44 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin
Evaluated 8 Feb 2005

A universal trend of amino acid gain and loss in protein evolution.
Jordan IK, Kondrashov FA, …, Kondrashov AS, Sunyaev S
Nature 2005 Feb 10 433(7026):633-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin / Jeffrey Thorne / Ulf Pettersson / Andrew Wilkie
Dissenters | Steven Henikoff
Author Response | Eugene Koonin
Evaluated 1 Feb 2005


Protein homology detection by HMM-HMM comparison.
Söding J
Bioinformatics 2005 Apr 1 21(7):951-60 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 21 Jan 2005

The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies.
Anantharaman V, Aravind L
Proteins 2004 Sep 1 56(4):795-807 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Nick Grishin
Evaluated 21 Jan 2005

A novel ADP- and zinc-binding fold from function-directed in vitro evolution.
Lo Surdo P, Walsh MA, Sollazzo M
Nat Struct Mol Biol 2004 Apr 11(4):382-3 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Burckhard Seelig / Nick Grishin
Evaluated 8 Apr 2004

Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis.
Wolf YI, Rogozin IB, Koonin EV
Genome Res 2004 Jan 14(1):29-36 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin / Arcady Mushegian / Alejandro Sanchez-Alvarado
Evaluated 23 Feb 2004

Design of a novel globular protein fold with atomic-level accuracy.
Kuhlman B, Dantas G, …, Stoddard BL, Baker D
Science 2003 Nov 21 302(5649):1364-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Kristina Downing / Gideon Schreiber / Rob Russell / Wolfgang Guba / Nick Grishin / Padmanabhan Balaram / Robert Kelley / Kevin Plaxco / Sachdev Sidhu
Evaluated 18 Dec 2003

Evolution and classification of P-loop kinases and related proteins.
Leipe DD, Koonin EV, Aravind L
J Mol Biol 2003 Oct 31 333(4):781-815 [abstract on PubMed] [related articles] [order article]
Selected by | Nick Grishin
Evaluated 17 Dec 2003

Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors.
Mirny LA, Gelfand MS
J Mol Biol 2002 Aug 2 321(1):7-20 [abstract on PubMed] [related articles] [order article]
Selected by | Rob Russell / Nick Grishin
Evaluated 24 Jan 2003

Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction.
Xiang Z, Soto CS, Honig B
Proc Natl Acad Sci U S A 2002 May 28 99(11):7432-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 11 Jun 2002

Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins.
Makarova KS, Ponomarev VA, Koonin EV
Genome Biol 2001 2(9):RESEARCH 0033 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin
Evaluated 29 Oct 2001

A simple algorithm to infer gene duplication and speciation events on a gene tree.
Zmasek CM, Eddy SR
Bioinformatics 2001 Sep 17(9):821-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Nick Grishin / Jonathan A Eisen
Evaluated 26 Oct 2001

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