Software

Grishin Lab Software and Services

ECOD

Evolutionary Classification of Protein Domains.
ECOD is a hierarchical classification of protein domains according to their evolutionary relationships.

ECOD is updated weekly by a combination of automtic methods and manual curation.

Reference: H. Cheng, R. D. Schaeffer, Y. Liao, L. N. Kinch, J. Pei, S. Shi, B. H. Kim, N. V. Grishin. (2014) "ECOD: An evolutionary classification of protein domains". PloS Computational Biology 10(12): e1003926 PMID: 25474468

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SFESA

Shift to Fix secondary structure ElementS in Alignments.
SFESA server refines pairwise protein sequence alignments using a combination of sequence and structural scoring by locally shifting secondary structure elements.

Reference: Tong J., Pei J., Otwinowski Z. & N.V. Grishin. (2015) "Refinement by shifting secondary structure elements improves sequence alignments". Proteins 83(3): 411-427 PMID: 25546158

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Pclust

Visualization of Protein cluster in a protein similarity network.
Pclust is a server to visualize the protein similarity network, placing emphasis on experimental studies (retrieved by Seq2Ref) and access to their full information in source databases.

Reference: Wenlin Li; Lisa N. Kinch; Nick V. Grishin. (2013) "Pclust: protein network visualization highlighting experimental data". Bioinformatics 29(20): 2647-2648 PMID: 23918248

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Seq2Ref

Sequences to References.
Seq2Ref is a web server designed to facilitate functional interpretation by retrieving and ranking the reference proteins in the BLAST result.

Reference: Li W, Cong Q, Kinch LN, Grishin NV. (2013) "Seq2Ref: a web server to facilitate functional interpretation". BMC Bioinformatics 14: 30 PMID: 23356573

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MESSA

MEta Server for protein Sequence Analysis.
MESSA is a meta sever that gathers predictions of local sequence features, spatial structure, function, homologous proteins, protein families and protein domains of a given protein sequence.

Reference: Cong Q, Grishin NV. (2012) "MESSA: MEta Server for Sequence Analysis". BMC Biology 10(1): 82 PMID: 23031578

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PROMALS3D

PROfile Multiple Alignment with predicted Local Structure and 3D constraints.
PROMALS3D is a multiple sequence and structure alignment program. It uses 3D structure superpositions where available and information from database searches and secondary structure predictions. According to our tests, PROMALS3D is currently the most accurate multiple alignment program available. Please let us know, if you find this is no longer the case.

Reference: J.Pei, B.H.Kim, and N.V.Grishin (2008) "PROMALS3D: a tool for multiple protein sequence and structure alignments." Nucleic Acids Res. 36(7): 2295-2300 PMID: 18287115

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QCS

Quality Control Score for structure prediction quality assessment.
Quality Control Score (QCS) is a new method to evaluate the quality of structure predictions, especially for template free structure prediction. It was developed to mimic visual inspction by human expert and it captures both global and local structural features, with emphasis on global topology.

Reference: Cong Q, Kinch LN, Pei J, Shi S, Grishin VN, Li W, Grishin NV. (2011) "An automatic method for CASP9 free modeling structure prediction assessment". Bioinformatics 27(24): 3371-3378 PMID: 21994223

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PALSSE

Predictive Assignment of Linear Secondary Structure Elements.
A program to delineate linear secondary structure elements from protein spatial structures.

Reference: I.Majumdar, S.S.Krishna, and N.V.Grishin (2005) "PALSSE: A program to delineate linear secondary structural elements from protein structures". BMC Bioinformatics 6: 202 PMID: 1190160

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COMPASS

COmparison of Multiple Protein sequence Alignments with assessment of Statistical Significance.
This program runs a search with submitted alignment (or sequence) as a query against a database of protein families.

Reference: R.I.Sadreyev and N.V.Grishin (2003) "COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance.” J. Mol. Biol 326(1): 317-336 PMID: 12547212

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ProCAIn

Protein profile Comparison with Assisting Information.
This program runs a search with submitted sequence (or alignment) as a query against a database of protein families.

Reference: Y.Wang, R.I.Sadreyev, and N.V.Grishin (2009) "PROCAIN: protein profile comparison with assisting information." Nucleic Acids Res. 37(11): 3522-3530 PMID: 19357092

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HorA

Homology or Aanalogy.
This server is for remote homology inference among protein domains with known 3D structures.

Reference: B.H.Kim, H.Cheng, and N.V.Grishin (2009) "HorA web server to infer homology between proteins using sequence and structural similarity." Nucleic Acids Res. 37(WSi): W532-W538 PMID: 19417074

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SCG

Self Consistency Grouping.

SCG clusters whose members are closer in rank to each other than to any member outside the cluster. SCG does not take any additional parameters and consequently does not impose any restriction on the size or the number of the clusters that it finds, since the natural boundaries of clusters are determined by the inconsistencies in the ranks.

Reference: Bong-Hyun Kim, Bhadrachalam Chitturi and Nick V Grishin. (2012) "Self consistency grouping: a stringent clustering method". BMC Bioinformatics 13(Suppl 13): S3 PMID: 23320864

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HangOut

HangOut removes "overhangs", which are erroneously extended during PSI-BLAST runs caused by long insertions or inserted domains, and builds clean profiles for those domains.

Reference: B.H. Kim, Q. Cong, N.V. Grishin (2010) "HangOut: generating clean PSI-BLAST profiles for domains containing long insertions". Bioinformatics 26(12): 1564-1565 PMID: 20413635

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ProSMoS

Protein Structure Motif Search.
Search for 3D patterns in protein structures, e.g. find all proteins with a fold defined by a user.

Reference: S-Y.Shi, B.Chitturi, and N.V.Grishin (2009) "ProSMoS server: a pattern-based search using interaction matrix representation of protein structures." Nucleic Acids Res. 37(WSi): W526-W531 PMID: 19420061

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PCMA

Profile Consistency Multiple sequence Alignment.
This program constructs a multiple sequence alignment given a set of protein sequences.

Reference: J.Pei, R.I.Sadreyev, and N.V.Grishin (2003) "PCMA: Fast and Accurate Multiple Sequence Alignment Based on Profile Consistency". Bioinformatics 19(3): 427-428. PMID: 12584134

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MUMMALS

MUltiple alignment with Multiple MAtch state models of Local Structure.
This program constructs a multiple sequence alignment given a set of protein sequences.

Reference: J. Pei and N.V.Grishin (2006) "MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information". Nucleic Acids Res 34(16): 4364-4374 PMID: 16936316

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PROMALS

PROfile Multiple Alignment with predicted Local Structure.
PROMALS constructs multiple protein sequence alignments using information from database searches and secondary structure predictions.

Reference: J.Pei and N.V.Grishin (2007) "PROMALS: towards accurate multiple sequence alignments of distantly related proteins". Bioinformatics. 23(7): 802-808 PMID: 17267437

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ANCESCON

ANCEStral sequence reCONstruction.

Reference: W.Cai, J.Pei, and N.V.Grishin (2004) "Reconstruction of ancestral protein sequences and its applications". BMC Evolutionary Biology 4(1): 33 PMID: 15377393

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WinDiso

WINdow-based DISOrder preditor.
WinDiso is a linear, sequence- and alignment-based predictor of disordered/unfolded regions in proteins. It has the capability of adjusting for the increased tendency for disorder at protein termini. The simple weighted window-based algorithm and careful optimization technique make this a good predictor to use when trying to avoid bias toward special cases. WinDiso was optimized using several thousand crystallographic structures. Analysis of its optimized parameters has provided insight into physical principles involved in order/disorder.

Reference: N.B.Holladay, L.N.Kinch, and N.V.Grishin (2007) "Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicity". Protein Science 16(10): 2140-2152 PMID: 17893360

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