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FRISC: The Faculty Research Interests Science Comparator
Nick Grishin, Ph.D.
Assistant Professor of Biochemistry
Biological
Chemistry
Phone: 214-648-3386
Fax: 214-648-9099
Building L; Room 4.247A
Email: grishin@chop.swmed.edu
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Selected Publications
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FRISC Statistics
Results - FULL MEDLINE:
Sequence-structure mapping errors in the PDB: OB-fold domains.
Ceslovas Venclovas ... Chulhee Kang
Protein Sci 2004 Jun; 13(6)1594-602.
Score: 0.492
QUASAR--scoring and ranking of sequence-structure alignments.
Fabian Birzele ... Ralf Zimmer
Bioinformatics 2005 Dec; 21(24)4425-6.
Score: 0.456
Evolutionary plasticity of protein families: coupling between sequence and structure variation.
Anna R Panchenko ... Thomas Madej
Proteins 2005 Nov; 61(3)535-44.
Score: 0.442
Sequence-structure specificity--how does an inverse folding approach work?
W P Hu ... J Skolnick
Protein Eng 1997 Apr; 10(4)317-31.
Score: 0.404
Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures.
C Ouzounis ... R Schneider
J Mol Biol 1993 Aug; 232(3)805-25.
Score: 0.403
A new progressive-iterative algorithm for multiple structure alignment.
Dmitry Lupyan ... Angel R Ortiz
Bioinformatics 2005 Aug; 21(15)3255-63.
Score: 0.403
Structural similarity to link sequence space: new potential superfamilies and implications for structural genomics.
Patrick Aloy ... Robert B Russell
Protein Sci 2002 May; 11(5)1101-16.
Score: 0.398
TRILOGY: Discovery of sequence-structure patterns across diverse proteins.
Philip Bradley ... Bonnie Berger
Proc Natl Acad Sci U S A 2002 Jun; 99(13)8500-5.
Score: 0.398
AS2TS system for protein structure modeling and analysis.
A Zemla ... D Barsky
Nucleic Acids Res 2005 Jul; 33(Web Server issue)W111-5.
Score: 0.394
Computational tools for protein modeling.
D Xu ... E C Uberbacher
Curr Protein Pept Sci 2000 Jul; 1(1)1-21.
Score: 0.391
Local sequence-structure motifs in RNA.
Rolf Backofen ... Sebastian Will
J Bioinform Comput Biol 2004 Dec; 2(4)681-98.
Score: 0.391
Evaluation of threading specificity and accuracy.
S H Bryant
Proteins 1996 Oct; 26(2)172-85.
Score: 0.390
Threading using neural nEtwork (TUNE): the measure of protein sequence-structure compatibility.
Kuang Lin ... William R Taylor
Bioinformatics 2002 Oct; 18(10)1350-7.
Score: 0.389
Computer analysis and structure prediction of nucleic acids and proteins.
M Kanehisa ... C DeLisi
Nucleic Acids Res 1984 Jan; 12(1 Pt 1)417-28.
Score: 0.389
Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment.
Ceslovas Venclovas ... Mindaugas Margelevicius
Proteins 2005 ; 61 Suppl 7()99-105.
Score: 0.385
Sequence variations within protein families are linearly related to structural variations.
Patrice Koehl ... Michael Levitt
J Mol Biol 2002 Oct; 323(3)551-62.
Score: 0.382
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons.
Sven Siebert ... Rolf Backofen
Bioinformatics 2005 Aug; 21(16)3352-9.
Score: 0.382
Decision support system for the evolutionary classification of protein structures.
L Holm ... C Sander
Proc Int Conf Intell Syst Mol Biol 1997 ; 5()140-6.
Score: 0.381
Towards a covering set of protein family profiles.
A Heger ... L Holm
Prog Biophys Mol Biol 2000 ; 73(5)321-37.
Score: 0.379
Protein fold recognition by sequence threading: tools and assessment techniques.
R T Miller ... J M Thornton
FASEB J 1996 Jan; 10(1)171-8.
Score: 0.377
Remotely related sequences and structures: analysis and predictive modelling.
W R Taylor
Trends Biotechnol 1994 May; 12(5)154-8.
Score: 0.377
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins.
Xin Yuan ... Christopher Bystroff
Bioinformatics 2005 Apr; 21(7)1010-9.
Score: 0.376
Structural classification of thioredoxin-like fold proteins.
Yuan Qi ... Nick V Grishin
Proteins 2005 Feb; 58(2)376-88.
Score: 0.370
Use of a database of structural alignments and phylogenetic trees in investigating the relationship between sequence and structural variability among homologous proteins.
S Balaji ... N Srinivasan
Protein Eng 2001 Apr; 14(4)219-26.
Score: 0.370
From genes to protein structure and function: novel applications of computational approaches in the genomic era.
J Skolnick ... J S Fetrow
Trends Biotechnol 2000 Jan; 18(1)34-9.
Score: 0.369
Protein design by optimization of a sequence-structure quality function.
S E Brenner ... A Berry
Proc Int Conf Intell Syst Mol Biol 1994 ; 2()44-52.
Score: 0.369
Structural features of prions explored by sequence analysis I. Sequence data.
J P Mornon ... I Callebaut
Cell Mol Life Sci 2002 Aug; 59(8)1366-76.
Score: 0.369
Prediction of protein function from protein sequence and structure.
James C Whisstock ... Arthur M Lesk
Q Rev Biophys 2003 Aug; 36(3)307-40.
Score: 0.368
Discovering sequence-structure motifs from protein segments and two applications.
Thomas Tang ... Ming Li
Pac Symp Biocomput 2005 ; ()370-81.
Score: 0.368
Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses.
N Goldman ... D T Jones
J Mol Biol 1996 Oct; 263(2)196-208.
Score: 0.364
Identification of homology in protein structure classification.
S Dietmann ... L Holm
Nat Struct Biol 2001 Nov; 8(11)953-7.
Score: 0.364
An Integrated Sequence-Structure Database incorporating matching mRNA sequence, amino acid sequence and protein three-dimensional structure data.
I A Adzhubei ... S Neidle
Nucleic Acids Res 1998 Jan; 26(1)327-31.
Score: 0.363
Structure prediction and modelling.
M B Swindells ... J M Thornton
Curr Opin Biotechnol 1991 Aug; 2(4)512-9.
Score: 0.362
An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence.
A S Yang ... B Honig
J Mol Biol 2000 Aug; 301(3)679-89.
Score: 0.362
Prediction of the structural similarity between spermidine/putrescine-binding protein and maltose-binding protein.
Y Matsuo ... K Nishikawa
FEBS Lett 1994 May; 345(1)23-6.
Score: 0.360
GeneSilico protein structure prediction meta-server.
Michal A Kurowski ... Janusz M Bujnicki
Nucleic Acids Res 2003 Jul; 31(13)3305-7.
Score: 0.360
SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments.
Julian Gough ... Cyrus Chothia
Nucleic Acids Res 2002 Jan; 30(1)268-72.
Score: 0.359
From structure to function: methods and applications.
Haim J Wolfson ... Ruth Nussinov
Curr Protein Pept Sci 2005 Apr; 6(2)171-83.
Score: 0.358
On the functional significance of electron density protein structure alignments.
Pere Constans
Proteins 2004 May; 55(3)646-55.
Score: 0.358
Molecular mimicry in channel-protein structure.
M Montal
Curr Opin Struct Biol 1995 Aug; 5(4)501-6.
Score: 0.357
Contemporary approaches to protein structure classification.
M B Swindells ... J M Thornton
Bioessays 1998 Nov; 20(11)884-91.
Score: 0.355
Touring protein fold space with Dali/FSSP.
L Holm ... C Sander
Nucleic Acids Res 1998 Jan; 26(1)316-9.
Score: 0.354
Structural genomics: computational methods for structure analysis.
Sharon Goldsmith-Fischman ... Barry Honig
Protein Sci 2003 Sep; 12(9)1813-21.
Score: 0.353
Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships.
Li Liao ... William Stafford Noble
J Comput Biol 2003 ; 10(6)857-68.
Score: 0.353
Fold change in evolution of protein structures.
N V Grishin
J Struct Biol 2001 May-Jun; 134(2-3)167-85.
Score: 0.351
GeneViTo: visualizing gene-product functional and structural features in genomic datasets.
Georgios S Vernikos ... Stavros J Hamodrakas
BMC Bioinformatics 2003 Oct; 4()53.
Score: 0.350
SCOP: a structural classification of proteins database for the investigation of sequences and structures.
A G Murzin ... C Chothia
J Mol Biol 1995 Apr; 247(4)536-40.
Score: 0.349
Recent progress in protein 3D structure comparison.
Oliviero Carugo ... Sandor Pongor
Curr Protein Pept Sci 2002 Aug; 3(4)441-9.
Score: 0.349
Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure.
Patricia C Babbitt ... Sean D Mooney
Pac Symp Biocomput 2005 ; ()319-21.
Score: 0.349
Protein structure prediction and biomolecular recognition: from protein sequence to peptidomimetic design with the human beta3 integrin.
R Casadio ... I Rossi
SAR QSAR Environ Res 2002 May-Jun; 13(3-4)473-86.
Score: 0.348
A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3.
S Dietmann ... L Holm
Nucleic Acids Res 2001 Jan; 29(1)55-7.
Score: 0.348
The FSSP database of structurally aligned protein fold families.
L Holm ... C Sander
Nucleic Acids Res 1994 Sep; 22(17)3600-9.
Score: 0.347
Statistics of sequence-structure threading.
S H Bryant ... S F Altschul
Curr Opin Struct Biol 1995 Apr; 5(2)236-44.
Score: 0.346
Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.
C A Wilson ... M Gerstein
J Mol Biol 2000 Mar; 297(1)233-49.
Score: 0.346
Protein structural similarities predicted by a sequence-structure compatibility method.
Y Matsuo ... K Nishikawa
Protein Sci 1994 Nov; 3(11)2055-63.
Score: 0.346
HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins.
C Bystroff ... D Baker
J Mol Biol 2000 Aug; 301(1)173-90.
Score: 0.346
Protein structure prediction and structural genomics.
D Baker ... A Sali
Science 2001 Oct; 294(5540)93-6.
Score: 0.346
Analysis of topological and nontopological structural similarities in the PDB: new examples with old structures.
N N Alexandrov ... D Fischer
Proteins 1996 Jul; 25(3)354-65.
Score: 0.346
Protein folds and families: sequence and structure alignments.
L Holm ... C Sander
Nucleic Acids Res 1999 Jan; 27(1)244-7.
Score: 0.345
Local structure-based sequence profile database for local and global protein structure predictions.
An-Suei Yang ... Lu-Yong Wang
Bioinformatics 2002 Dec; 18(12)1650-7.
Score: 0.344
Evolution of protein sequences and structures.
T C Wood ... W R Pearson
J Mol Biol 1999 Aug; 291(4)977-95.
Score: 0.344
Prediction of local structure in proteins using a library of sequence-structure motifs.
C Bystroff ... D Baker
J Mol Biol 1998 Aug; 281(3)565-77.
Score: 0.343
Protein sequence analysis in silico: application of structure-based bioinformatics to genomic initiatives.
David Michalovich ... Richard Fagan
Curr Opin Pharmacol 2002 Oct; 2(5)574-80.
Score: 0.342
SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence.
C Z Cai ... Y Z Chen
Nucleic Acids Res 2003 Jul; 31(13)3692-7.
Score: 0.341
Protein structure prediction. Implications for the biologist.
G Deléage ... C Geourjon
Biochimie 1997 Nov; 79(11)681-6.
Score: 0.341
JEvTrace: refinement and variations of the evolutionary trace in JAVA.
Marcin P Joachimiak ... Fred E Cohen
Genome Biol 2002 ; 3(12)RESEARCH0077.
Score: 0.341
Protein sequence-structure compatibility criteria in terms of statistical hypothesis testing.
S Sunyaev ... V Tumanyan
Protein Eng 1997 Jun; 10(6)635-46.
Score: 0.340
Protein structure prediction: inroads to biology.
Donald Petrey ... Barry Honig
Mol Cell 2005 Dec; 20(6)811-9.
Score: 0.340
Integrating protein secondary structure prediction and multiple sequence alignment.
V A Simossis ... J Heringa
Curr Protein Pept Sci 2004 Aug; 5(4)249-66.
Score: 0.340
Phylogenomic inference of protein molecular function: advances and challenges.
Kimmen Sjölander
Bioinformatics 2004 Jan; 20(2)170-9.
Score: 0.339
Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design.
Gong Cheng ... David Baker
Nucleic Acids Res 2005 ; 33(18)5861-7.
Score: 0.339
A database of protein structure families with common folding motifs.
L Holm ... G Vriend
Protein Sci 1992 Dec; 1(12)1691-8.
Score: 0.337
Automated protein design and sequence optimisation: scoring functions and the search problem.
A P Cootes ... A E Torda
Curr Protein Pept Sci 2000 Nov; 1(3)255-71.
Score: 0.337
A comparison of sequence and structure protein domain families as a basis for structural genomics.
A Elofsson ... E L Sonnhammer
Bioinformatics 1999 Jun; 15(6)480-500.
Score: 0.337
A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment.
R H Lathrop ... J V White
Bull Math Biol 1998 Nov; 60(6)1039-71.
Score: 0.336
Distant homology recognition using structural classification of proteins.
A G Murzin ... A Bateman
Proteins 1997 ; Suppl 1()105-12.
Score: 0.336
Review: protein design--where we were, where we are, where we're going.
N Pokala ... T M Handel
J Struct Biol 2001 May-Jun; 134(2-3)269-81.
Score: 0.335
Computation of conformational entropy from protein sequences using the machine-learning method--application to the study of the relationship between structural conservation and local structural stability.
Shao-Wei Huang ... Jenn-Kang Hwang
Proteins 2005 Jun; 59(4)802-9.
Score: 0.335
The structural alignment between two proteins: is there a unique answer?
A Godzik
Protein Sci 1996 Jul; 5(7)1325-38.
Score: 0.335
Local protein sequence similarity does not imply a structural relationship.
M J Sternberg ... S A Islam
Protein Eng 1990 Dec; 4(2)125-31.
Score: 0.334
Managing biological sequence and protein structure data.
Zhiping Weng
OMICS 2003 ; 7(1)25-6.
Score: 0.334
Inverse sequence similarity in proteins and its relation to the three-dimensional fold.
R Preissner ... C Frömmel
FEBS Lett 1997 Sep; 414(2)425-9.
Score: 0.334
The role of protein structure in genomics.
F S Domingues ... M J Sippl
FEBS Lett 2000 Jun; 476(1-2)98-102.
Score: 0.333
Optimal classification of protein sequences and selection of representative sets from multiple alignments: application to homologous families and lessons for structural genomics.
A C May
Protein Eng 2001 Apr; 14(4)209-17.
Score: 0.333
Exploiting protein structure data to explore the evolution of protein function and biological complexity.
Russell L Marsden ... Christine A Orengo
Philos Trans R Soc Lond B Biol Sci 2006 Mar; 361(1467)425-40.
Score: 0.333
Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci.
Michael A Chapman ... Berthold Göttgens
Genome Res 2004 Feb; 14(2)313-8.
Score: 0.333
SCOP database in 2004: refinements integrate structure and sequence family data.
Antonina Andreeva ... Alexey G Murzin
Nucleic Acids Res 2004 Jan; 32(Database issue)D226-9.
Score: 0.332
Protein databases and software on BIONET.
S Maulik
Protein Seq Data Anal 1989 Feb; 2(2)111-4.
Score: 0.332
Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions.
Yao-Ming Huang ... Christopher Bystroff
Bioinformatics 2006 Feb; 22(4)413-22.
Score: 0.331
Assessing a novel approach for predicting local 3D protein structures from sequence.
Cristina Benros ... Serge Hazout
Proteins 2006 Mar; 62(4)865-80.
Score: 0.330
Structural Modelling of the Sm-like Protein Hfq from Escherichia coli.
Véronique Arluison ... Philippe Régnier
J Mol Biol 2002 Jul; 320(4)705-12.
Score: 0.330
Protein folds, functions and evolution.
J M Thornton ... F M Pearl
J Mol Biol 1999 Oct; 293(2)333-42.
Score: 0.330
Local sequence-structure correlations in proteins.
C Bystroff ... D Baker
Curr Opin Biotechnol 1996 Aug; 7(4)417-21.
Score: 0.329
Phylogeny as a guide to structure and function of membrane transport proteins.
Abraham B Chang ... Milton H Saier
Mol Membr Biol 2004 May-Jun; 21(3)171-81.
Score: 0.329
Estimates of statistical significance for comparison of individual positions in multiple sequence alignments.
Ruslan I Sadreyev ... Nick V Grishin
BMC Bioinformatics 2004 Aug; 5()106.
Score: 0.329
Compound library development guided by protein structure similarity clustering and natural product structure.
Marcus A Koch ... Herbert Waldmann
Proc Natl Acad Sci U S A 2004 Nov; 101(48)16721-6.
Score: 0.329
Analysis of protein sequence/structure similarity relationships.
Hin Hark Gan ... Tamar Schlick
Biophys J 2002 Nov; 83(5)2781-91.
Score: 0.328
Integrated tools for structural and sequence alignment and analysis.
C C Huang ... T E Klein
Pac Symp Biocomput 2000 ; ()230-41.
Score: 0.328
DMAPS: a database of multiple alignments for protein structures.
Chittibabu Guda ... Ilya N Shindyalov
Nucleic Acids Res 2006 Jan; 34(Database issue)D273-6.
Score: 0.328
A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.
D D Pollock ... M P Cummings
Mol Biol Evol 2000 Dec; 17(12)1776-88.
Score: 0.328
From protein structure to function.
C A Orengo ... J M Thornton
Curr Opin Struct Biol 1999 Jun; 9(3)374-82.
Score: 0.327
Database of structural motifs in proteins.
K Guruprasad ... G R Kumar
Bioinformatics 2000 Apr; 16(4)372-5.
Score: 0.327
MMDB: Entrez's 3D structure database.
A Marchler-Bauer ... S H Bryant
Nucleic Acids Res 1999 Jan; 27(1)240-3.
Score: 0.327
Insights into protein function through large-scale computational analysis of sequence and structure.
M Weir ... J Overington
Trends Biotechnol 2001 Oct; 19(10 Suppl)S61-6.
Score: 0.327
Failed to fetch article title! Article may not be available.
Score: 0.326
Five hierarchical levels of sequence-structure correlation in proteins.
Christopher Bystroff ... Xin Yuan
Appl Bioinformatics 2004 ; 3(2-3)97-104.
Score: 0.326
Connecting the protein structure universe by using sparse recurring fragments.
Iddo Friedberg ... Adam Godzik
Structure 2005 Aug; 13(8)1213-24.
Score: 0.325
Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships.
Nicola D Gold ... Richard M Jackson
J Mol Biol 2006 Feb; 355(5)1112-24.
Score: 0.325
Order, disorder, and flexibility: prediction from protein sequence.
Lilia M Iakoucheva ... A Keith Dunker
Structure 2003 Nov; 11(11)1316-7.
Score: 0.324
Alignment algorithm for homology modeling and threading.
N N Alexandrov ... R Luethy
Protein Sci 1998 Feb; 7(2)254-8.
Score: 0.324
A sequence property approach to searching protein databases.
U Hobohm ... C Sander
J Mol Biol 1995 Aug; 251(3)390-9.
Score: 0.323
Dali/FSSP classification of three-dimensional protein folds.
L Holm ... C Sander
Nucleic Acids Res 1997 Jan; 25(1)231-4.
Score: 0.323
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.
Sudhir Kumar ... Masatoshi Nei
Brief Bioinform 2004 Jun; 5(2)150-63.
Score: 0.323
The CATH Database provides insights into protein structure/function relationships.
C A Orengo ... J M Thornton
Nucleic Acids Res 1999 Jan; 27(1)275-9.
Score: 0.322
Computational methods for protein secondary structure prediction using multiple sequence alignments.
J Heringa
Curr Protein Pept Sci 2000 Nov; 1(3)273-301.
Score: 0.322
New tools for protein sequence analysis.
F Sakiyama
Trends Biotechnol 1990 Oct; 8(10)282-8.
Score: 0.322
On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations.
W Kabsch ... C Sander
Proc Natl Acad Sci U S A 1984 Feb; 81(4)1075-8.
Score: 0.322
Consistency matrices: quantified structure alignments for sets of related proteins.
Ivo Van Walle ... Lode Wyns
Proteins 2003 Apr; 51(1)1-9.
Score: 0.321
Prediction of protein function in the absence of significant sequence similarity.
Paul D Dobson ... Andrew J Doig
Curr Med Chem 2004 Aug; 11(16)2135-42.
Score: 0.321
A computational pipeline for protein structure prediction and analysis at genome scale.
Manesh Shah ... Ying Xu
Bioinformatics 2003 Oct; 19(15)1985-96.
Score: 0.321
Measurements of protein sequence-structure correlations.
Gavin E Crooks ... Steven E Brenner
Proteins 2004 Dec; 57(4)804-10.
Score: 0.321
Multiple sequence alignments.
Iain M Wallace ... Desmond G Higgins
Curr Opin Struct Biol 2005 Jun; 15(3)261-6.
Score: 0.320
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction.
Jun-tao Guo ... Ying Xu
Nucleic Acids Res 2004 Jul; 32(Web Server issue)W522-5.
Score: 0.320
Modeling three-dimensional protein structures for amino acid sequences of the CASP3 experiment using sequence-derived predictions.
D Fischer
Proteins 1999 ; Suppl 3()61-5.
Score: 0.320
The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs.
Sam Griffiths-Jones ... Alex Bateman
Bioinformatics 2002 Sep; 18(9)1243-9.
Score: 0.319
MSAT: a multiple sequence alignment tool based on TOPS.
Te Ren ... David Gilbert
Appl Bioinformatics 2004 ; 3(2-3)149-58.
Score: 0.319
Sequence-structure specificity of a knowledge based energy function at the secondary structure level.
D Xu ... E C Uberbacher
Bioinformatics 2000 Mar; 16(3)257-68.
Score: 0.318
Structural similarity of loops in protein families: toward the understanding of protein evolution.
Anna R Panchenko ... Thomas Madej
BMC Evol Biol 2005 ; 5(1)10.
Score: 0.318
SAD--a normalized structural alignment database: improving sequence-structure alignments.
Brian Marsden ... Ruben Abagyan
Bioinformatics 2004 Oct; 20(15)2333-44.
Score: 0.318
Comparison of sequence and structure alignments for protein domains.
Aron Marchler-Bauer ... Stephen H Bryant
Proteins 2002 Aug; 48(3)439-46.
Score: 0.318
Towards a reliable objective function for multiple sequence alignments.
J D Thompson ... O Poch
J Mol Biol 2001 Dec; 314(4)937-51.
Score: 0.318
Analysis and prediction of functional sub-types from protein sequence alignments.
S S Hannenhalli ... R B Russell
J Mol Biol 2000 Oct; 303(1)61-76.
Score: 0.318
Creation and analysis of protein multiple sequence alignments.
G J Barton
Methods Biochem Anal 2001 ; 43()215-32.
Score: 0.318
Protein folds in channel structure.
M Montal
Curr Opin Struct Biol 1996 Aug; 6(4)499-510.
Score: 0.318
A functional hierarchical organization of the protein sequence space.
Noam Kaplan ... Michal Linial
BMC Bioinformatics 2004 ; 5()196.
Score: 0.317
PASS2: an automated database of protein alignments organised as structural superfamilies.
Anirban Bhaduri ... Ramanathan Sowdhamini
BMC Bioinformatics 2004 Apr; 5()35.
Score: 0.317
A comprehensive set of sequence analysis programs for the VAX.
J Devereux ... O Smithies
Nucleic Acids Res 1984 Jan; 12(1 Pt 1)387-95.
Score: 0.317
Database of homology-derived protein structures and the structural meaning of sequence alignment.
C Sander ... R Schneider
Proteins 1991 ; 9(1)56-68.
Score: 0.317
Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis.
D Milburn ... J M Thornton
Protein Eng 1998 Oct; 11(10)855-9.
Score: 0.317
How similar must a template protein be for homology modeling by side-chain packing methods?
S Y Chung ... S Subbiah
Pac Symp Biocomput 1996 ; ()126-41.
Score: 0.316
On the evolution of structure in aminoacyl-tRNA synthetases.
Patrick O'Donoghue ... Zaida Luthey-Schulten
Microbiol Mol Biol Rev 2003 Dec; 67(4)550-73.
Score: 0.316
Identification of homologous core structures.
Y Matsuo ... S H Bryant
Proteins 1999 Apr; 35(1)70-9.
Score: 0.316
Sisyphus and prediction of protein structure.
B Rost ... S O'Donoghue
Comput Appl Biosci 1997 Aug; 13(4)345-56.
Score: 0.315
MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison.
Angel R Ortiz ... Osvaldo Olmea
Protein Sci 2002 Nov; 11(11)2606-21.
Score: 0.315
Identification and classification of protein fold families.
C A Orengo ... J M Thornton
Protein Eng 1993 Jul; 6(5)485-500.
Score: 0.315
Picasso: generating a covering set of protein family profiles.
A Heger ... L Holm
Bioinformatics 2001 Mar; 17(3)272-9.
Score: 0.315
A new method for building protein conformations from sequence alignments with homologues of known structure.
T F Havel ... M E Snow
J Mol Biol 1991 Jan; 217(1)1-7.
Score: 0.315
On the classification and evolution of protein modules.
H Hegyi ... P Bork
J Protein Chem 1997 Jul; 16(5)545-51.
Score: 0.315
Identification of predictive sequence motifs limited by protein structure data base size.
M J Rooman ... S J Wodak
Nature 1988 Sep; 335(6185)45-9.
Score: 0.314
Unification of protein families.
L Holm
Curr Opin Struct Biol 1998 Jun; 8(3)372-9.
Score: 0.314
From sequence to structure to literature: the protocol approach to bioinformation.
O P Wu ... S Subbiah
Pac Symp Biocomput 1998 ; ()747-58.
Score: 0.314
FSSA: a novel method for identifying functional signatures from structural alignments.
Kai Wang ... Ram Samudrala
Bioinformatics 2005 Jul; 21(13)2969-77.
Score: 0.314
Protein threading by PROSPECT: a prediction experiment in CASP3.
Y Xu ... G Zhang
Protein Eng 1999 Nov; 12(11)899-907.
Score: 0.314
Bioinformatic tools for DNA/protein sequence analysis, functional assignment of genes and protein classification.
B H Rehm
Appl Microbiol Biotechnol 2001 Dec; 57(5-6)579-92.
Score: 0.314
Exploring protein domain structure.
J C Ison
Brief Bioinform 2000 Sep; 1(3)305-12.
Score: 0.313
Expanding the nitrogen regulatory protein superfamily: Homology detection at below random sequence identity.
Lisa N Kinch ... Nick V Grishin
Proteins 2002 Jul; 48(1)75-84.
Score: 0.313
Protein fold recognition.
D Jones ... J Thornton
J Comput Aided Mol Des 1993 Aug; 7(4)439-56.
Score: 0.313
Functional annotation by identification of local surface similarities: a novel tool for structural genomics.
Fabrizio Ferrè ... Manuela Helmer-Citterich
BMC Bioinformatics 2005 ; 6()194.
Score: 0.313
Artificial neural networks for molecular sequence analysis.
C H Wu
Comput Chem 1997 ; 21(4)237-56.
Score: 0.313
Practical lessons from protein structure prediction.
Krzysztof Ginalski ... Leszek Rychlewski
Nucleic Acids Res 2005 ; 33(6)1874-91.
Score: 0.312
BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark.
Julie D Thompson ... Olivier Poch
Proteins 2005 Oct; 61(1)127-36.
Score: 0.312
GLASS: a tool to visualize protein structure prediction data in three dimensions and evaluate their consistency.
R Leplae ... A Tramontano
Proteins 1998 Mar; 30(4)339-51.
Score: 0.312
The PIR-International Protein Sequence Database.
W C Barker ... C Wu
Nucleic Acids Res 1999 Jan; 27(1)39-43.
Score: 0.311
Protein function from sequence and structure data.
Francisco S Domingues ... Thomas Lengauer
Appl Bioinformatics 2003 ; 2(1)3-12.
Score: 0.311
Protein structure similarities.
P Koehl
Curr Opin Struct Biol 2001 Jun; 11(3)348-53.
Score: 0.311
Bioinformatics methods to predict protein structure and function. A practical approach.
Yvonne J K Edwards ... Amanda Cottage
Mol Biotechnol 2003 Feb; 23(2)139-66.
Score: 0.311
Identification of similar regions of protein structures using integrated sequence and structure analysis tools.
Brandon Peters ... Sean Mooney
BMC Struct Biol 2006 ; 6()4.
Score: 0.311
Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs.
V Kunin ... S Pietrokovski
J Mol Biol 2001 Mar; 307(3)939-49.
Score: 0.311
Quantification of secondary structure prediction improvement using multiple alignments.
J M Levin ... J Garnier
Protein Eng 1993 Nov; 6(8)849-54.
Score: 0.311
Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices.
Andrew E Torda ... Thomas Huber
Nucleic Acids Res 2004 Jul; 32(Web Server issue)W532-5.
Score: 0.311
SimShift: identifying structural similarities from NMR chemical shifts.
Simon W Ginzinger ... Johannes Fischer
Bioinformatics 2006 Feb; 22(4)460-5.
Score: 0.311
Sequence-structure homology recognition by iterative alignment refinement and comparative modeling.
M G Williams ... P I de Bakker
Proteins 2001 ; Suppl 5()92-7.
Score: 0.311
ProTarget: automatic prediction of protein structure novelty.
Ori Sasson ... Michal Linial
Nucleic Acids Res 2005 Jul; 33(Web Server issue)W81-4.
Score: 0.310
Structure and sequence relationships in the lipocalins and related proteins.
D R Flower ... T K Attwood
Protein Sci 1993 May; 2(5)753-61.
Score: 0.310
A simple topological representation of protein structure: implications for new, fast, and robust structural classification.
David L Bostick ... Iosif I Vaisman
Proteins 2004 Aug; 56(3)487-501.
Score: 0.310
Tools and resources for identifying protein families, domains and motifs.
Nicola J Mulder ... Rolf Apweiler
Genome Biol 2002 ; 3(1)REVIEWS2001.
Score: 0.310
An approach to improving multiple alignments of protein sequences using predicted secondary structure.
A J Jennings ... M J Sternberg
Protein Eng 2001 Apr; 14(4)227-31.
Score: 0.310
Toward more meaningful hierarchical classification of protein three-dimensional structures.
A C May
Proteins 1999 Oct; 37(1)20-9.
Score: 0.310
Prediction of protein structure from sequence.
M J Sternberg ... M J Zvelebil
Eur J Cancer 1990 ; 26(11-12)1163-6.
Score: 0.310
The ASTRAL compendium for protein structure and sequence analysis.
S E Brenner ... M Levitt
Nucleic Acids Res 2000 Jan; 28(1)254-6.
Score: 0.310
An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments.
A S Yang ... B Honig
J Mol Biol 2000 Aug; 301(3)691-711.
Score: 0.310
[Recent trends in protein structural studies]
K Titani ... N Hayashi
Rinsho Byori 1998 May; 46(5)450-5.
Score: 0.309
Progress in protein structure prediction?
B Rost ... C Sander
Trends Biochem Sci 1993 Apr; 18(4)120-3.
Score: 0.309
Computational identification of residues that modulate voltage sensitivity of voltage-gated potassium channels.
Bin Li ... Warren J Gallin
BMC Struct Biol 2005 ; 5()16.
Score: 0.309
Multiple model approach--dealing with alignment ambiguities in protein modeling.
K Pawłowski ... A Godzik
Pac Symp Biocomput 1997 ; ()328-39.
Score: 0.309
Search for structural similarity in proteins.
Jacek Leluk ... Irena Roterman
Bioinformatics 2003 Jan; 19(1)117-24.
Score: 0.309
Déjà vu all over again: finding and analyzing protein structure similarities.
Michael L Sierk ... Gerard J Kleywegt
Structure 2004 Dec; 12(12)2103-11.
Score: 0.309
Reconstruction of ancestral protein sequences and its applications.
Wei Cai ... Nick V Grishin
BMC Evol Biol 2004 Sep; 4()33.
Score: 0.308
Why are some proteins structures so common?
S Govindarajan ... R A Goldstein
Proc Natl Acad Sci U S A 1996 Apr; 93(8)3341-5.
Score: 0.308
Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels.
R B Russell ... G J Barton
Proteins 1992 Oct; 14(2)309-23.
Score: 0.308
Predicting protein function from sequence and structural data.
James D Watson ... Janet M Thornton
Curr Opin Struct Biol 2005 Jun; 15(3)275-84.
Score: 0.308
Mismatch string kernels for discriminative protein classification.
Christina S Leslie ... William Stafford Noble
Bioinformatics 2004 Mar; 20(4)467-76.
Score: 0.308
Quick selection of representative protein chain sets based on customizable requirements.
T Noguchi ... Y Akiyama
Bioinformatics 2000 Jun; 16(6)520-6.
Score: 0.308
Expectations from structural genomics revisited: an analysis of structural genomics targets.
Mansoor A S Saqi ... David L Wild
Am J Pharmacogenomics 2005 ; 5(5)339-42.
Score: 0.308
Scoring docking models with evolutionary information.
Michael Tress ... Alfonso Valencia
Proteins 2005 Aug; 60(2)275-80.
Score: 0.307
From fold to function predictions: an apoptosis regulator protein BID.
K Pawłowski ... A Godzik
Comput Chem 2000 May; 24(3-4)511-7.
Score: 0.307
Prediction of functional sites in proteins using conserved functional group analysis.
C Axel Innis ... R Sowdhamini
J Mol Biol 2004 Apr; 337(4)1053-68.
Score: 0.307
Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources.
Jannik N Andersen ... Nicholas K Tonks
Methods 2005 Jan; 35(1)90-114.
Score: 0.307
Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches.
R Samudrala ... R Davis
Pac Symp Biocomput 2000 ; ()179-90.
Score: 0.307
TopDraw: a sketchpad for protein structure topology cartoons.
Charles S Bond
Bioinformatics 2003 Jan; 19(2)311-2.
Score: 0.306
S4: structure-based sequence alignments of SCOP superfamilies.
James Casbon ... Mansoor A S Saqi
Nucleic Acids Res 2005 Jan; 33(Database issue)D219-22.
Score: 0.306
Putting microarrays in a context: integrated analysis of diverse biological data.
Olga G Troyanskaya
Brief Bioinform 2005 Mar; 6(1)34-43.
Score: 0.306
Integrated web service for improving alignment quality based on segments comparison.
Dariusz Plewczynski ... Adam Godzik
BMC Bioinformatics 2004 Jul; 5()98.
Score: 0.306
Secondary structure prediction for modelling by homology.
P E Boscott ... W G Richards
Protein Eng 1993 Apr; 6(3)261-6.
Score: 0.306
Building an automated classification of DNA-binding protein domains.
Julia V Ponomarenko ... Ilya N Shindyalov
Bioinformatics 2002 ; 18 Suppl 2()S192-201.
Score: 0.305
Computer modeling studies of the structure of a repressor.
W F Anderson ... M Cygler
Biosystems 1985 ; 18(1)3-14.
Score: 0.305
SESAM: a relational database for structure and sequence of macromolecules.
M Huysmans ... S J Wodak
Proteins 1991 ; 11(1)59-76.
Score: 0.305
Site-specific molecular design and its relevance to pharmacogenomics and chemical biology.
D Bailey ... P Dean
Pharmacogenomics J 2001 ; 1(1)38-47.
Score: 0.304
Sequence-dependent DNA structure.
C A Hunter
Bioessays 1996 Feb; 18(2)157-62.
Score: 0.304
Nucleic acid and protein sequence databases.
G G Kneale ... M J Bishop
Comput Appl Biosci 1985 ; 1(1)11-7.
Score: 0.304
DBAli: a database of protein structure alignments.
M A Martí-Renom ... A Sali
Bioinformatics 2001 Aug; 17(8)746-7.
Score: 0.304
Statistical significance of protein structure prediction by threading.
L A Mirny ... E I Shakhnovich
Proc Natl Acad Sci U S A 2000 Aug; 97(18)9978-83.
Score: 0.304
A molecular model of the carbohydrate recognition domain of a rat macrophage lectin and analysis of its binding site.
J Bajorath
J Mol Graph 1996 Oct; 14(5)297-301, 283-4.
Score: 0.304
The proteome: structure, function and evolution.
Keiran Fleming ... Michael J E Sternberg
Philos Trans R Soc Lond B Biol Sci 2006 Mar; 361(1467)441-51.
Score: 0.303
Evolution of function in protein superfamilies, from a structural perspective.
A E Todd ... J M Thornton
J Mol Biol 2001 Apr; 307(4)1113-43.
Score: 0.303
Update on protein structure prediction: results of the 1995 IRBM workshop.
T Hubbard ... A Tramontano
Fold Des 1996 ; 1(3)R55-63.
Score: 0.303
Local structure prediction with local structure-based sequence profiles.
An-Suei Yang ... Lu-yong Wang
Bioinformatics 2003 Jul; 19(10)1267-74.
Score: 0.303
PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways.
Natalia Maltsev ... Mark D'Souza
Nucleic Acids Res 2006 Jan; 34(Database issue)D369-72.
Score: 0.303
Non-random usage of 'degenerate' codons is related to protein three-dimensional structure.
A A Adzhubei ... S Neidle
FEBS Lett 1996 Dec; 399(1-2)78-82.
Score: 0.303
Functional implications from crystal structures of the conserved Bacillus subtilis protein Maf with and without dUTP.
G Minasov ... M Egli
Proc Natl Acad Sci U S A 2000 Jun; 97(12)6328-33.
Score: 0.303
Extracting hydrogen-bond signature patterns from protein structure data.
Tejasvini Prasad ... Nagasuma Chandra
Appl Bioinformatics 2004 ; 3(2-3)125-35.
Score: 0.303
A functional superfamily of sodium/solute symporters.
J Reizer ... M H Saier
Biochim Biophys Acta 1994 Jun; 1197(2)133-66.
Score: 0.302
Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins.
R Landgraf ... D Eisenberg
J Mol Biol 2001 Apr; 307(5)1487-502.
Score: 0.302
A robust method to detect structural and functional remote homologues.
Ori Shachar ... Michal Linial
Proteins 2004 Nov; 57(3)531-8.
Score: 0.302
Optimum superimposition of protein structures: ambiguities and implications.
Z K Feng ... M J Sippl
Fold Des 1996 ; 1(2)123-32.
Score: 0.302
Accurate and scalable identification of functional sites by evolutionary tracing.
Olivier Lichtarge ... Ivana Mihalek
J Struct Funct Genomics 2003 ; 4(2-3)159-66.
Score: 0.302
Visualization techniques for genomic data.
Ann E Loraine ... Gregg A Helt
Proc IEEE Comput Soc Bioinform Conf 2002 ; 1()321-6.
Score: 0.301
Genome-based structural biology.
D Frishman ... H W Mewes
Prog Biophys Mol Biol 1999 ; 72(1)1-17.
Score: 0.301
A map of the protein space--an automatic hierarchical classification of all protein sequences.
G Yona ... M Linial
Proc Int Conf Intell Syst Mol Biol 1998 ; 6()212-21.
Score: 0.301
Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
I N Shindyalov ... C Sander
Protein Eng 1994 Mar; 7(3)349-58.
Score: 0.301
Protein structure: a new strategy for sequence analysis.
W R Gray
Nature 1968 Dec; 220(5174)1300-4.
Score: 0.300
An alternative view of protein fold space.
I N Shindyalov ... P E Bourne
Proteins 2000 Feb; 38(3)247-60.
Score: 0.300
Medical target prediction from genome sequence: combining different sequence analysis algorithms with expert knowledge and input from artificial intelligence approaches.
T Dandekar ... S Schmidt
Comput Chem 2001 Dec; 26(1)15-21.
Score: 0.300
Protein structure prediction.
B Al-Lazikani ... B Honig
Curr Opin Chem Biol 2001 Feb; 5(1)51-6.
Score: 0.300
Enhanced genome annotation using structural profiles in the program 3D-PSSM.
L A Kelley ... M J Sternberg
J Mol Biol 2000 Jun; 299(2)499-520.
Score: 0.299
Comparative modeling of CASP4 target proteins: combining results of sequence search with three-dimensional structure assessment.
C Venclovas
Proteins 2001 ; Suppl 5()47-54.
Score: 0.299
ABC: software for interactive browsing of genomic multiple sequence alignment data.
Gregory M Cooper ... Arend Sidow
BMC Bioinformatics 2004 Dec; 5()192.
Score: 0.299
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds.
Ruslan I Sadreyev ... Nick V Grishin
BMC Struct Biol 2006 ; 6()6.
Score: 0.299
Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools.
N C Kyrpides ... R Overbeek
Nucleic Acids Res 2000 Nov; 28(22)4573-6.
Score: 0.299
Insights from MHC-bound peptides.
Hanah Margalit ... Yael Altuvia
Novartis Found Symp 2003 ; 254()77-90; discussion 91-101, 216-22, 250-2.
Score: 0.299
The FSSP database: fold classification based on structure-structure alignment of proteins.
L Holm ... C Sander
Nucleic Acids Res 1996 Jan; 24(1)206-9.
Score: 0.298
EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments.
Jean-Christophe Gelly ... Jérôme Gracy
BMC Bioinformatics 2005 ; 6()4.
Score: 0.298
[Use of multiple structural alignment for recognizing the type of protein spatial architecture]
Sh R Siuniaev ... V G Tumanian
Biofizika 1999 Jul-Aug; 44(4)620-3.
Score: 0.298
PIRSF: family classification system at the Protein Information Resource.
Cathy H Wu ... Winona C Barker
Nucleic Acids Res 2004 Jan; 32(Database issue)D112-4.
Score: 0.297
Divergent evolution within protein superfolds inferred from profile-based phylogenetics.
Douglas L Theobald ... Deborah S Wuttke
J Mol Biol 2005 Dec; 354(3)722-37.
Score: 0.297
Theoretical analysis of alternative splice forms using computational methods.
Stéphanie Boué ... Ina Koch
Bioinformatics 2002 ; 18 Suppl 2()S65-73.
Score: 0.297
Interaction profile-based protein classification of death domain.
Drew Lett ... Frederic Pio
BMC Bioinformatics 2004 Jun; 5()75.
Score: 0.297
Clustering of proximal sequence space for the identification of protein families.
Federico Abascal ... Alfonso Valencia
Bioinformatics 2002 Jul; 18(7)908-21.
Score: 0.297
Protein structure prediction and analysis using the Robetta server.
David E Kim ... David Baker
Nucleic Acids Res 2004 Jul; 32(Web Server issue)W526-31.
Score: 0.296
Vector NTI, a balanced all-in-one sequence analysis suite.
Guoqing Lu ... Etsuko N Moriyama
Brief Bioinform 2004 Dec; 5(4)378-88.
Score: 0.296
Using fold recognition to search for useful proteins: Bayesian approach to fold recognition.
Jadwiga R Bienkowska
Brief Bioinform 2002 Mar; 3(1)45-58.
Score: 0.296
Structural characterization of genomes by large scale sequence-structure threading.
Artem Cherkasov ... Steven J M Jones
BMC Bioinformatics 2004 Apr; 5()37.
Score: 0.296
Alignment and structure prediction of divergent protein families: periplasmic and outer membrane proteins of bacterial efflux pumps.
J M Johnson ... G M Church
J Mol Biol 1999 Apr; 287(3)695-715.
Score: 0.296
Progress of 1D protein structure prediction at last.
B Rost ... C Sander
Proteins 1995 Nov; 23(3)295-300.
Score: 0.296
Identifying sequence-structure pairs undetected by sequence alignments.
S Miyazawa ... R L Jernigan
Protein Eng 2000 Jul; 13(7)459-75.
Score: 0.296
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.
Rachel Kolodny ... Michael Levitt
J Mol Biol 2005 Mar; 346(4)1173-88.
Score: 0.296
Predicting protein structure classes from function predictions.
I Sommer ... T Lengauer
Bioinformatics 2004 Mar; 20(5)770-6.
Score: 0.295
New approaches in molecular structure prediction.
G Böhm
Biophys Chem 1996 Mar; 59(1-2)1-32.
Score: 0.295
Evolutionary profiles from the QR factorization of multiple sequence alignments.
Anurag Sethi ... Zaida Luthey-Schulten
Proc Natl Acad Sci U S A 2005 Mar; 102(11)4045-50.
Score: 0.295
Integrated databanks access and sequence/structure analysis services at the PBIL.
Guy Perrière ... Gilbert Deléage
Nucleic Acids Res 2003 Jul; 31(13)3393-9.
Score: 0.295
Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology.
Julia V Ponomarenko ... Ilya N Shindyalov
Proteins 2005 Mar; 58(4)855-65.
Score: 0.294
PALI-a database of Phylogeny and AL
