Software

Grishin Lab Software, Databases and Services

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. (): [Epub] Apr 7; 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. (): [Epub] May 5; PMID: 19417074

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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. (): [Epub] May 6; 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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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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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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AL2CO

ALignment to COnservation.
AL2CO calculates positional conservation for a multiple protein sequence alignment.

Reference: J.Pei and N.V.Grishin (2001) "AL2CO: calculation of positional conservation in a protein sequence alignment." Bioinformatics. 17(8): 700-712 PMID: 11524371

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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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Structural Classification of Zinc Fingers

Zinc fingers are small protein domains in which zinc plays a structural role contributing to the stability of the domain. Zinc fingers are structurally diverse and are present among proteins that perform a broad range of functions in various cellular processes. Zinc fingers typically function as interaction modules and bind to a wide variety of compounds, such as nucleic acids, proteins and small molecules.

We have made a comprehensive classification of zinc finger spatial structures. The zinc finger database has been constructed by manual examination of zinc finger domain structures. We find that each available zinc finger structure can be placed into one of eight fold groups that we define based on the structural properties in the vicinity of the zinc-binding site. Evolutionary relatedness of proteins within fold groups is not implied, but each group is divided into families of potential homologues.

Reference: S.S.Krishna, I.Majumdar, and N.V.Grishin (2003) "Structural classification of zinc fingers". Nucleic Acid Research 31(2): 532-550 PMID: 12527760

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MALIDUP

Manual ALIgnments of DUPlicated domains.
A database of pairwise, structure-base alignments for homologous domains originated by internal duplication.

Reference: H.Cheng, B.H.Kim, and N.V.Grishin (2007) "MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs". Proteins 70(4): 1162-1166 PMID: 17932926

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MALISAM

Manual ALIgnments of Structurally Analogous Motifs.
A database of pairwise, structure-based alignments for structurally analogous but evolutionarily unrelated motifs in proteins.

Reference: H.Cheng, B.H.Kim, and N.V.Grishin (2007) "MALISAM: a database of structurally analogous motifs". Nucleic Acids 36(Database Issue): D211-217 PMID: 17855399

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MultiDom

MultiDomain proteins.
A database of domain definitions for Multidomain protein class in SCOP

Reference: I.Majumdar, L.N.Kinch, and N.V.Grishin (2009) "A database of domain definitions for proteins with complex interdomain geometry." PLoS ONE 4(4): e5084 Apr 8; PMID: 19352501

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