Nick V. Grishin

Orcid: 0000-0003-4108-1153

According to our database1, Nick V. Grishin authored at least 50 papers between 2001 and 2024.

Collaborative distances:
  • Dijkstra number2 of five.
  • Erdős number3 of four.

Timeline

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Links

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Bibliography

2024
ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2.
PLoS Comput. Biol., February, 2024

2022
DisEnrich: database of enriched regions in human dark proteome.
Bioinform., 2022

2020
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type.
PLoS Comput. Biol., 2020

pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes.
Bioinform., 2020

The Potential of Single Cell RNA-Sequencing Data for the Prediction of Gastric Cancer Serum Biomarkers.
Proceedings of the Mathematical and Computational Oncology, 2020

2019
Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways.
PLoS Comput. Biol., 2019

2018
A sequence family database built on ECOD structural domains.
Bioinform., 2018

2017
ECOD: new developments in the evolutionary classification of domains.
Nucleic Acids Res., 2017

2016
Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.
PLoS Comput. Biol., 2016

2015
SFESA: a web server for pairwise alignment refinement by secondary structure shifts.
BMC Bioinform., 2015

LocNES: a computational tool for locating classical NESs in CRM1 cargo proteins.
Bioinform., 2015

2014
ECOD: An Evolutionary Classification of Protein Domains.
PLoS Comput. Biol., 2014

2013
Seq2Ref: a web server to facilitate functional interpretation.
BMC Bioinform., 2013

Pclust: protein network visualization highlighting experimental data.
Bioinform., 2013

M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci.
Bioinform., 2013

Defining and predicting structurally conserved regions in protein superfamilies.
Bioinform., 2013

2012
Self consistency grouping: a stringent clustering method.
BMC Bioinform., 2012

2011
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions.
J. Comput. Chem., 2011

An automatic method for CASP9 free modeling structure prediction assessment.
Bioinform., 2011

2010
HangOut: generating clean PSI-BLAST profiles for domains with long insertions.
Bioinform., 2010

Structural Differences between Proteins with Similar Sequences.
Proceedings of the 10th IEEE International Conference on Bioinformatics and Bioengineering, 2010

2009
ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.
Nucleic Acids Res., 2009

COMPASS server for homology detection: improved statistical accuracy, speed and functionality.
Nucleic Acids Res., 2009

HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res., 2009

Considering scores between unrelated proteins in the search database improves profile comparison.
BMC Bioinform., 2009

PROCAIN server for remote protein sequence similarity search.
Bioinform., 2009

Structure similarity measure with penalty for close non-equivalent residues.
Bioinform., 2009

Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.
Bioinform., 2009

Analysis of CASP8 targets, predictions and assessment methods.
Database J. Biol. Databases Curation, 2009

2008
PROMALS3D web server for accurate multiple protein sequence and structure alignments.
Nucleic Acids Res., 2008

MALISAM: a database of structurally analogous motifs in proteins.
Nucleic Acids Res., 2008

Statistics of Random Protein Superpositions: <i>p</i>-Values for Pairwise Structure Alignment.
J. Comput. Biol., 2008

2007
COMPASS server for remote homology inference.
Nucleic Acids Res., 2007

PROMALS web server for accurate multiple protein sequence alignments.
Nucleic Acids Res., 2007

A comprehensive system for evaluation of remote sequence similarity detection.
BMC Bioinform., 2007

Searching for three-dimensional secondary structural patterns in proteins with ProSMoS.
Bioinform., 2007

PROMALS: towards accurate multiple sequence alignments of distantly related proteins.
Bioinform., 2007

2006
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios.
Bioinform., 2006

The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria.
Bioinform., 2006

2005
PALSSE: A program to delineate linear secondary structural elements from protein structures.
BMC Bioinform., 2005

Structural drift: a possible path to protein fold change.
Bioinform., 2005

2004
Detecting distant homology with Meta-BASIC.
Nucleic Acids Res., 2004

Estimates of statistical significance for comparison of individual positions in multiple sequence alignments.
BMC Bioinform., 2004

SCOPmap: Automated assignment of protein structures to evolutionary superfamilies.
BMC Bioinform., 2004

Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs.
Bioinform., 2004

PCOAT: positional correlation analysis using multiple methods.
Bioinform., 2004

2003
PCMA: fast and accurate multiple sequence alignment based on profile consistency.
Bioinform., 2003

Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments.
Bioinform., 2003

2002
Euclidian space and grouping of biological objects.
Bioinform., 2002

2001
AL2CO: calculation of positional conservation in a protein sequence alignment.
Bioinform., 2001


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