AL2CO: calculation of positional conservation in a protein sequence alignment. - Jimin Pei; Nick V. Grishin (Bioinform., 2001)

PCMA: fast and accurate multiple sequence alignment based on profile consistency. - Jimin Pei; Ruslan Sadreyev; Nick V. Grishin (Bioinform., 2003)

Prediction of functional specificity determinants from protein sequences using log-likelihood ratios. - Jimin Pei; Wei Cai; Lisa N. Kinch; Nick V. Grishin (Bioinform., 2006)

PROMALS: towards accurate multiple sequence alignments of distantly related proteins. - Jimin Pei; Nick V. Grishin (Bioinform., 2007)

PROMALS web server for accurate multiple protein sequence alignments. - Jimin Pei; Bong-Hyun Kim; Ming Tang; Nick V. Grishin (Nucleic Acids Res., 2007)

PROMALS3D web server for accurate multiple protein sequence and structure alignments. - Jimin Pei; Ming Tang; Nick V. Grishin (Nucleic Acids Res., 2008)

Analysis of CASP8 targets, predictions and assessment methods. - Shuoyong Shi; Jimin Pei; Ruslan Sadreyev; Lisa N. Kinch; Indraneel Majumdar; Jing Tong; Hua Cheng; Bong-Hyun Kim; Nick V. Grishin (Database J. Biol. Databases Curation, 2009)

An automatic method for CASP9 free modeling structure prediction assessment. - Qian Cong; Lisa N. Kinch; Jimin Pei; Shuoyong Shi; Vyacheslav N. Grishin; Wenlin Li; Nick V. Grishin (Bioinform., 2011)

Defining and predicting structurally conserved regions in protein superfamilies. - Ivan K. Huang; Jimin Pei; Nick V. Grishin (Bioinform., 2013)

ECOD: An Evolutionary Classification of Protein Domains. - Hua Cheng; R. Dustin Schaeffer; Yuxing Liao; Lisa N. Kinch; Jimin Pei; Shuoyong Shi; Bong-Hyun Kim; Nick V. Grishin (PLoS Comput. Biol., 2014)

LocNES: a computational tool for locating classical NESs in CRM1 cargo proteins. - Darui Xu; Kara Marquis; Jimin Pei; Szu-Chin Fu; Tolga Cagatay; Nick V. Grishin; Yuh Min Chook (Bioinform., 2015)

SFESA: a web server for pairwise alignment refinement by secondary structure shifts. - Jing Tong; Jimin Pei; Nick V. Grishin (BMC Bioinform., 2015)

A sequence family database built on ECOD structural domains. - Yuxing Liao; R. Dustin Schaeffer; Jimin Pei; Nick V. Grishin (Bioinform., 2018)

pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes. - Yoonji Lee; Jordan M. Baumhardt; Jimin Pei; Yuh Min Chook; Nick V. Grishin (Bioinform., 2020)

Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. - Jimin Pei; Lisa N. Kinch; Zbyszek Otwinowski; Nick V. Grishin (PLoS Comput. Biol., 2020)

DisEnrich: database of enriched regions in human dark proteome. - Kirill E. Medvedev; Jimin Pei; Nick V. Grishin (Bioinform., 2022)

Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling. - Jimin Pei; Jing Zhang 115; Qian Cong (Bioinform., 2022)

AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold. - Jimin Pei; Qian Cong (Database J. Biol. Databases Curation, 2023)