Nick V. Grishin

53 papers C 1Journal 51Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
ECOD: Classification of domains in AFDB Swiss-Prot structure predictions.
PLoS Comput. Biol.
R. Dustin Schaeffer, Jing Zhang, Qian Cong, Nick V. Grishin
2025 J jnl
Leveraging AI to explore structural contexts of post-translational modifications in drug binding.
J. Cheminformatics
Kirill E. Medvedev, R. Dustin Schaeffer, Nick V. Grishin
2025 J jnl
Using evolutionary context to classify difficult protein folds.
PLoS Comput. Biol.
Jimin Pei, R. Dustin Schaeffer, Qian Cong, Nick V. Grishin
2024 J jnl
ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2.
PLoS Comput. Biol.
R. Dustin Schaeffer, Jing Zhang, Kirill E. Medvedev, Lisa N. Kinch, Qian Cong, Nick V. Grishin
2022 J jnl
DisEnrich: database of enriched regions in human dark proteome.
Bioinform.
Kirill E. Medvedev, Jimin Pei, Nick V. Grishin
2020 J jnl
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type.
PLoS Comput. Biol.
Jimin Pei, Lisa N. Kinch, Zbyszek Otwinowski, Nick V. Grishin
2020 — conf
The Potential of Single Cell RNA-Sequencing Data for the Prediction of Gastric Cancer Serum Biomarkers.
ISMCO
Kirill E. Medvedev, Anna V. Savelyeva, Aditya Bagrodia, Nick V. Grishin
2020 J jnl
pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes.
Bioinform.
Yoonji Lee, Jordan M. Baumhardt, Jimin Pei, Yuh Min Chook, Nick V. Grishin
2019 J jnl
Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways.
PLoS Comput. Biol.
Kirill E. Medvedev, Lisa N. Kinch, R. Dustin Schaeffer, Nick V. Grishin
2018 J jnl
A sequence family database built on ECOD structural domains.
Bioinform.
Yuxing Liao, R. Dustin Schaeffer, Jimin Pei, Nick V. Grishin
2017 J jnl
ECOD: new developments in the evolutionary classification of domains.
Nucleic Acids Res.
R. Dustin Schaeffer, Yuxing Liao, Hua Cheng, Nick V. Grishin
2016 J jnl
Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.
PLoS Comput. Biol.
Raquel Bromberg, Nick V. Grishin, Zbyszek Otwinowski
2015 J jnl
LocNES: a computational tool for locating classical NESs in CRM1 cargo proteins.
Bioinform.
Darui Xu, Kara Marquis, Jimin Pei, Szu-Chin Fu, Tolga Cagatay, Nick V. Grishin, Yuh Min Chook
2015 J jnl
SFESA: a web server for pairwise alignment refinement by secondary structure shifts.
BMC Bioinform.
Jing Tong, Jimin Pei, Nick V. Grishin
2014 J jnl
ECOD: An Evolutionary Classification of Protein Domains.
PLoS Comput. Biol.
Hua Cheng, R. Dustin Schaeffer, Yuxing Liao, Lisa N. Kinch, Jimin Pei, Shuoyong Shi, Bong-Hyun Kim, Nick V. Grishin
2013 J jnl
Defining and predicting structurally conserved regions in protein superfamilies.
Bioinform.
Ivan K. Huang, Jimin Pei, Nick V. Grishin
2013 J jnl
M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci.
Bioinform.
Renkai Ji, Qian Cong, Wenlin Li, Nick V. Grishin
2013 J jnl
Pclust: protein network visualization highlighting experimental data.
Bioinform.
Wenlin Li, Lisa N. Kinch, Nick V. Grishin
2013 J jnl
Seq2Ref: a web server to facilitate functional interpretation.
BMC Bioinform.
Wenlin Li, Qian Cong, Lisa N. Kinch, Nick V. Grishin
2012 J jnl
Self consistency grouping: a stringent clustering method.
BMC Bioinform.
Bong-Hyun Kim, Bhadrachalam Chitturi, Nick V. Grishin
2011 J jnl
An automatic method for CASP9 free modeling structure prediction assessment.
Bioinform.
Qian Cong, Lisa N. Kinch, Jimin Pei, Shuoyong Shi, Vyacheslav N. Grishin, Wenlin Li, Nick V. Grishin
2011 J jnl
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions.
J. Comput. Chem.
Shide Liang, Yaoqi Zhou, Nick V. Grishin, Daron M. Standley
2010 J jnl
HangOut: generating clean PSI-BLAST profiles for domains with long insertions.
Bioinform.
Bong-Hyun Kim, Qian Cong, Nick V. Grishin
2010 C conf
Structural Differences between Proteins with Similar Sequences.
BIBE
Qian Cong, Bong-Hyun Kim, Lisa N. Kinch, Nick V. Grishin
2009 J jnl
Analysis of CASP8 targets, predictions and assessment methods.
Database J. Biol. Databases Curation
Shuoyong Shi, Jimin Pei, Ruslan Sadreyev, Lisa N. Kinch, Indraneel Majumdar, Jing Tong, Hua Cheng, Bong-Hyun Kim, Nick V. Grishin
2009 J jnl
COMPASS server for homology detection: improved statistical accuracy, speed and functionality.
Nucleic Acids Res.
Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V. Grishin
2009 J jnl
Considering scores between unrelated proteins in the search database improves profile comparison.
BMC Bioinform.
Ruslan Sadreyev, Yong Wang, Nick V. Grishin
2009 J jnl
HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res.
Bong-Hyun Kim, Hua Cheng, Nick V. Grishin
2009 J jnl
PROCAIN server for remote protein sequence similarity search.
Bioinform.
Yong Wang, Ruslan Sadreyev, Nick V. Grishin
2009 J jnl
Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.
Bioinform.
Ruslan Sadreyev, Jamison D. Feramisco, Hensin Tsao, Nick V. Grishin
2009 J jnl
ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.
Nucleic Acids Res.
Shuoyong Shi, Bhadrachalam Chitturi, Nick V. Grishin
2009 J jnl
Structure similarity measure with penalty for close non-equivalent residues.
Bioinform.
Ruslan Sadreyev, Shuoyong Shi, David Baker, Nick V. Grishin
2008 J jnl
MALISAM: a database of structurally analogous motifs in proteins.
Nucleic Acids Res.
Hua Cheng, Bong-Hyun Kim, Nick V. Grishin
2008 J jnl
PROMALS3D web server for accurate multiple protein sequence and structure alignments.
Nucleic Acids Res.
Jimin Pei, Ming Tang, Nick V. Grishin
2008 J jnl
Statistics of Random Protein Superpositions:
J. Comput. Biol.
James O. Wrabl, Nick V. Grishin
2007 J jnl
A comprehensive system for evaluation of remote sequence similarity detection.
BMC Bioinform.
Yuan Qi, Ruslan Sadreyev, Yong Wang, Bong-Hyun Kim, Nick V. Grishin
2007 J jnl
COMPASS server for remote homology inference.
Nucleic Acids Res.
Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V. Grishin
2007 J jnl
PROMALS web server for accurate multiple protein sequence alignments.
Nucleic Acids Res.
Jimin Pei, Bong-Hyun Kim, Ming Tang, Nick V. Grishin
2007 J jnl
PROMALS: towards accurate multiple sequence alignments of distantly related proteins.
Bioinform.
Jimin Pei, Nick V. Grishin
2007 J jnl
Searching for three-dimensional secondary structural patterns in proteins with ProSMoS.
Bioinform.
Shuoyong Shi, Yi Zhong, Indraneel Majumdar, S. Sri Krishna, Nick V. Grishin
2006 J jnl
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios.
Bioinform.
Jimin Pei, Wei Cai, Lisa N. Kinch, Nick V. Grishin
2006 J jnl
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria.
Bioinform.
Kira S. Makarova, Nick V. Grishin, Eugene V. Koonin
2005 J jnl
PALSSE: A program to delineate linear secondary structural elements from protein structures.
BMC Bioinform.
Indraneel Majumdar, S. Sri Krishna, Nick V. Grishin
2005 J jnl
Structural drift: a possible path to protein fold change.
Bioinform.
S. Sri Krishna, Nick V. Grishin
2004 J jnl
Detecting distant homology with Meta-BASIC.
Nucleic Acids Res.
Krzysztof Ginalski, Marcin von Grotthuss, Nick V. Grishin, Leszek Rychlewski
2004 J jnl
Estimates of statistical significance for comparison of individual positions in multiple sequence alignments.
BMC Bioinform.
Ruslan Sadreyev, Nick V. Grishin
2004 J jnl
PCOAT: positional correlation analysis using multiple methods.
Bioinform.
Yuan Qi, Nick V. Grishin
2004 J jnl
Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs.
Bioinform.
Ruslan Sadreyev, Nick V. Grishin
2004 J jnl
SCOPmap: Automated assignment of protein structures to evolutionary superfamilies.
BMC Bioinform.
Sara Cheek, Yuan Qi, S. Sri Krishna, Lisa N. Kinch, Nick V. Grishin
2003 J jnl
PCMA: fast and accurate multiple sequence alignment based on profile consistency.
Bioinform.
Jimin Pei, Ruslan Sadreyev, Nick V. Grishin
2003 J jnl
Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments.
Bioinform.
David Mittelman, Ruslan Sadreyev, Nick V. Grishin
2002 J jnl
Euclidian space and grouping of biological objects.
Bioinform.
Vyacheslav N. Grishin, Nick V. Grishin
2001 J jnl
AL2CO: calculation of positional conservation in a protein sequence alignment.
Bioinform.
Jimin Pei, Nick V. Grishin