Nick V. Grishin

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 11

Top Topics

Secondary Structure

Top Venues

PLoS Comput. Biol.

Nucleic Acids Res.

Publications

R. Dustin Schaeffer, Jing Zhang, Kirill E. Medvedev, Lisa N. Kinch, Qian Cong, Nick V. Grishin
ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2. PLoS Comput. Biol. 20 (2) (2024)
Kirill E. Medvedev, Jimin Pei, Nick V. Grishin
DisEnrich: database of enriched regions in human dark proteome. Bioinform. 38 (7) (2022)
Jimin Pei, Lisa N. Kinch, Zbyszek Otwinowski, Nick V. Grishin
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PLoS Comput. Biol. 16 (5) (2020)
Yoonji Lee, Jordan M. Baumhardt, Jimin Pei, Yuh Min Chook, Nick V. Grishin
pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes. Bioinform. 36 (3) (2020)
Kirill E. Medvedev, Anna V. Savelyeva, Aditya Bagrodia, Nick V. Grishin
The Potential of Single Cell RNA-Sequencing Data for the Prediction of Gastric Cancer Serum Biomarkers. ISMCO (2020)
Kirill E. Medvedev, Lisa N. Kinch, R. Dustin Schaeffer, Nick V. Grishin
Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways. PLoS Comput. Biol. 15 (12) (2019)
Yuxing Liao, R. Dustin Schaeffer, Jimin Pei, Nick V. Grishin
A sequence family database built on ECOD structural domains. Bioinform. 34 (17) (2018)
R. Dustin Schaeffer, Yuxing Liao, Hua Cheng, Nick V. Grishin
ECOD: new developments in the evolutionary classification of domains. Nucleic Acids Res. 45 (Database-Issue) (2017)
Raquel Bromberg, Nick V. Grishin, Zbyszek Otwinowski
Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer. PLoS Comput. Biol. 12 (6) (2016)
Jing Tong, Jimin Pei, Nick V. Grishin
SFESA: a web server for pairwise alignment refinement by secondary structure shifts. BMC Bioinform. 16 (2015)
Darui Xu, Kara Marquis, Jimin Pei, Szu-Chin Fu, Tolga Cagatay, Nick V. Grishin, Yuh Min Chook
LocNES: a computational tool for locating classical NESs in CRM1 cargo proteins. Bioinform. 31 (9) (2015)
Hua Cheng, R. Dustin Schaeffer, Yuxing Liao, Lisa N. Kinch, Jimin Pei, Shuoyong Shi, Bong-Hyun Kim, Nick V. Grishin
ECOD: An Evolutionary Classification of Protein Domains. PLoS Comput. Biol. 10 (12) (2014)
Ivan K. Huang, Jimin Pei, Nick V. Grishin
Defining and predicting structurally conserved regions in protein superfamilies. Bioinform. 29 (2) (2013)
Wenlin Li, Lisa N. Kinch, Nick V. Grishin
Pclust: protein network visualization highlighting experimental data. Bioinform. 29 (20) (2013)
Wenlin Li, Qian Cong, Lisa N. Kinch, Nick V. Grishin
Seq2Ref: a web server to facilitate functional interpretation. BMC Bioinform. 14 (2013)
Renkai Ji, Qian Cong, Wenlin Li, Nick V. Grishin
M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci. Bioinform. 29 (22) (2013)
Bong-Hyun Kim, Bhadrachalam Chitturi, Nick V. Grishin
Self consistency grouping: a stringent clustering method. BMC Bioinform. 13 (S-13) (2012)
Shide Liang, Yaoqi Zhou, Nick V. Grishin, Daron M. Standley
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. J. Comput. Chem. 32 (8) (2011)
Qian Cong, Lisa N. Kinch, Jimin Pei, Shuoyong Shi, Vyacheslav N. Grishin, Wenlin Li, Nick V. Grishin
An automatic method for CASP9 free modeling structure prediction assessment. Bioinform. 27 (24) (2011)
Qian Cong, Bong-Hyun Kim, Lisa N. Kinch, Nick V. Grishin
Structural Differences between Proteins with Similar Sequences. BIBE (2010)
Bong-Hyun Kim, Qian Cong, Nick V. Grishin
HangOut: generating clean PSI-BLAST profiles for domains with long insertions. Bioinform. 26 (12) (2010)
Shuoyong Shi, Bhadrachalam Chitturi, Nick V. Grishin
ProSMoS server: a pattern-based search using interaction matrix representation of protein structures. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V. Grishin
COMPASS server for homology detection: improved statistical accuracy, speed and functionality. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Bong-Hyun Kim, Hua Cheng, Nick V. Grishin
HorA web server to infer homology between proteins using sequence and structural similarity. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Shuoyong Shi, Jimin Pei, Ruslan Sadreyev, Lisa N. Kinch, Indraneel Majumdar, Jing Tong, Hua Cheng, Bong-Hyun Kim, Nick V. Grishin
Analysis of CASP8 targets, predictions and assessment methods. Database J. Biol. Databases Curation 2009 (2009)
Ruslan Sadreyev, Yong Wang, Nick V. Grishin
Considering scores between unrelated proteins in the search database improves profile comparison. BMC Bioinform. 10 (2009)
Yong Wang, Ruslan Sadreyev, Nick V. Grishin
PROCAIN server for remote protein sequence similarity search. Bioinform. 25 (16) (2009)
Ruslan Sadreyev, Shuoyong Shi, David Baker, Nick V. Grishin
Structure similarity measure with penalty for close non-equivalent residues. Bioinform. 25 (10) (2009)
Ruslan Sadreyev, Jamison D. Feramisco, Hensin Tsao, Nick V. Grishin
Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways. Bioinform. 25 (22) (2009)
Hua Cheng, Bong-Hyun Kim, Nick V. Grishin
MALISAM: a database of structurally analogous motifs in proteins. Nucleic Acids Res. 36 (Database-Issue) (2008)
Jimin Pei, Ming Tang, Nick V. Grishin
PROMALS3D web server for accurate multiple protein sequence and structure alignments. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
James O. Wrabl, Nick V. Grishin
-Values for Pairwise Structure Alignment. J. Comput. Biol. 15 (3) (2008)
Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V. Grishin
COMPASS server for remote homology inference. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Jimin Pei, Nick V. Grishin
PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinform. 23 (7) (2007)
Yuan Qi, Ruslan Sadreyev, Yong Wang, Bong-Hyun Kim, Nick V. Grishin
A comprehensive system for evaluation of remote sequence similarity detection. BMC Bioinform. 8 (2007)
Jimin Pei, Bong-Hyun Kim, Ming Tang, Nick V. Grishin
PROMALS web server for accurate multiple protein sequence alignments. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Shuoyong Shi, Yi Zhong, Indraneel Majumdar, S. Sri Krishna, Nick V. Grishin
Searching for three-dimensional secondary structural patterns in proteins with ProSMoS. Bioinform. 23 (11) (2007)
Jimin Pei, Wei Cai, Lisa N. Kinch, Nick V. Grishin
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios. Bioinform. 22 (2) (2006)
Kira S. Makarova, Nick V. Grishin, Eugene V. Koonin
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. Bioinform. 22 (21) (2006)
S. Sri Krishna, Nick V. Grishin
Structural drift: a possible path to protein fold change. Bioinform. 21 (8) (2005)
Indraneel Majumdar, S. Sri Krishna, Nick V. Grishin
PALSSE: A program to delineate linear secondary structural elements from protein structures. BMC Bioinform. 6 (2005)
Yuan Qi, Nick V. Grishin
PCOAT: positional correlation analysis using multiple methods. Bioinform. 20 (18) (2004)
Sara Cheek, Yuan Qi, S. Sri Krishna, Lisa N. Kinch, Nick V. Grishin
SCOPmap: Automated assignment of protein structures to evolutionary superfamilies. BMC Bioinform. 5 (2004)
Ruslan Sadreyev, Nick V. Grishin
Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs. Bioinform. 20 (6) (2004)
Ruslan Sadreyev, Nick V. Grishin
Estimates of statistical significance for comparison of individual positions in multiple sequence alignments. BMC Bioinform. 5 (2004)
Krzysztof Ginalski, Marcin von Grotthuss, Nick V. Grishin, Leszek Rychlewski
Detecting distant homology with Meta-BASIC. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
David Mittelman, Ruslan Sadreyev, Nick V. Grishin
Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinform. 19 (12) (2003)
Jimin Pei, Ruslan Sadreyev, Nick V. Grishin
PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinform. 19 (3) (2003)
Vyacheslav N. Grishin, Nick V. Grishin
Euclidian space and grouping of biological objects. Bioinform. 18 (11) (2002)
Jimin Pei, Nick V. Grishin
AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinform. 17 (8) (2001)