Class information for:
Level 1: CORRELATED MUTATIONS//DIRECT COUPLING ANALYSIS//INVERSE ISING PROBLEM

Basic class information
Class id #P Avg. number of
references		 Database coverage
of references
17055 620 37.0 74%


Bar chart of Publication_year

Last years might be incomplete

Hierarchy of classes
The table includes all classes above and classes immediately below the current class.


Cluster id Level Cluster label #P
0 4 BIOCHEMISTRY & MOLECULAR BIOLOGY//CELL BIOLOGY//ONCOLOGY 4064930
219 3       PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS//PROTEIN FOLDING//PROTEIN STRUCTURE PREDICTION 50409
365 2             PROTEIN STRUCTURE PREDICTION//PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS//PSEUDO AMINO ACID COMPOSITION 17331
17055 1                   CORRELATED MUTATIONS//DIRECT COUPLING ANALYSIS//INVERSE ISING PROBLEM 620

Terms with highest relevance score


rank Term termType Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 CORRELATED MUTATIONS authKW 395345 3% 47% 17
2 DIRECT COUPLING ANALYSIS authKW 253281 1% 86% 6
3 INVERSE ISING PROBLEM authKW 246247 1% 100% 5
4 CONTACT PREDICTION authKW 246237 2% 50% 10
5 CONTACT MAP authKW 222209 3% 24% 19
6 CONTACT MAP PREDICTION authKW 175888 1% 71% 5
7 PROTEIN CONTACT MAP authKW 157596 1% 80% 4
8 RESIDUE RESIDUE CONTACT authKW 157596 1% 80% 4
9 COEVOLVING RESIDUES authKW 147748 0% 100% 3
10 CORRELATED SUBSTITUTIONS authKW 147748 0% 100% 3

Web of Science journal categories


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 Mathematical & Computational Biology 9850 23% 0% 144
2 Biochemical Research Methods 3159 24% 0% 150
3 Physics, Mathematical 1125 12% 0% 77
4 Biotechnology & Applied Microbiology 891 17% 0% 106
5 Biochemistry & Molecular Biology 884 34% 0% 208
6 Biophysics 544 12% 0% 72
7 Computer Science, Artificial Intelligence 352 7% 0% 42
8 Physics, Fluids & Plasmas 209 5% 0% 31
9 Evolutionary Biology 189 4% 0% 25
10 Computer Science, Interdisciplinary Applications 98 4% 0% 25

Address terms


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 GENOM MICROORGANISMES 105054 1% 27% 8
2 BIOL COMPUTAT QUANTITAT BIOL PARIS SEINE 98499 0% 100% 2
3 UMR 7238 86386 2% 18% 10
4 EVOLUTIONARY GENET BIOINFORMAT 65660 1% 33% 4
5 TAO INRIA 55402 0% 38% 3
6 ABIOT ST SGRP INTEGRAT SYST BIOL 49249 0% 100% 1
7 ACCESS LINNAEUS KTH 49249 0% 100% 1
8 BIOCOMPU GRP 49249 0% 100% 1
9 BIOINFORMACT UNIT 49249 0% 100% 1
10 BIOINFORMAT GRP COMP SCI 49249 0% 100% 1

Journals


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 14911 7% 1% 44
2 BIOINFORMATICS 13952 9% 1% 55
3 JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT 6660 4% 1% 22
4 BMC STRUCTURAL BIOLOGY 6276 1% 2% 8
5 BMC BIOINFORMATICS 6269 5% 0% 31
6 PLOS COMPUTATIONAL BIOLOGY 4669 3% 0% 21
7 PROTEIN ENGINEERING 3118 2% 1% 12
8 MOLECULAR BIOLOGY AND EVOLUTION 1965 2% 0% 15
9 NEURAL NETWORKS 1548 2% 0% 10
10 INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES 1429 0% 1% 3

Author Key Words


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class		 LCSH search Wikipedia search
1 CORRELATED MUTATIONS 395345 3% 47% 17 Search CORRELATED+MUTATIONS Search CORRELATED+MUTATIONS
2 DIRECT COUPLING ANALYSIS 253281 1% 86% 6 Search DIRECT+COUPLING+ANALYSIS Search DIRECT+COUPLING+ANALYSIS
3 INVERSE ISING PROBLEM 246247 1% 100% 5 Search INVERSE+ISING+PROBLEM Search INVERSE+ISING+PROBLEM
4 CONTACT PREDICTION 246237 2% 50% 10 Search CONTACT+PREDICTION Search CONTACT+PREDICTION
5 CONTACT MAP 222209 3% 24% 19 Search CONTACT+MAP Search CONTACT+MAP
6 CONTACT MAP PREDICTION 175888 1% 71% 5 Search CONTACT+MAP+PREDICTION Search CONTACT+MAP+PREDICTION
7 PROTEIN CONTACT MAP 157596 1% 80% 4 Search PROTEIN+CONTACT+MAP Search PROTEIN+CONTACT+MAP
8 RESIDUE RESIDUE CONTACT 157596 1% 80% 4 Search RESIDUE+RESIDUE+CONTACT Search RESIDUE+RESIDUE+CONTACT
9 COEVOLVING RESIDUES 147748 0% 100% 3 Search COEVOLVING+RESIDUES Search COEVOLVING+RESIDUES
10 CORRELATED SUBSTITUTIONS 147748 0% 100% 3 Search CORRELATED+SUBSTITUTIONS Search CORRELATED+SUBSTITUTIONS

Core articles
The table includes core articles in the class. The following variables is taken into account for the relevance score of an article in a cluster c:
(1) Number of references referring to publications in the class.
(2) Share of total number of active references referring to publications in the class.
(3) Age of the article. New articles get higher score than old articles.
(4) Citation rate, normalized to year.


Rank Reference # ref.
in cl.		 Shr. of ref. in
cl.		 Citations
1 XU, HS , LI, XQ , ZHANG, ZD , SONG, JN , (2013) IDENTIFYING COEVOLUTION BETWEEN AMINO ACID RESIDUES IN PROTEIN FAMILIES: ADVANCES IN THE IMPROVEMENT AND EVALUATION OF CORRELATED MUTATION ALGORITHMS.CURRENT BIOINFORMATICS. VOL. 8. ISSUE 2. P. 148-160 54 71% 1
2 EKEBERG, M , LOVKVIST, C , LAN, YH , WEIGT, M , AURELL, E , (2013) IMPROVED CONTACT PREDICTION IN PROTEINS: USING PSEUDOLIKELIHOODS TO INFER POTTS MODELS.PHYSICAL REVIEW E. VOL. 87. ISSUE 1. P. - 29 78% 80
3 EKEBERG, M , HARTONEN, T , AURELL, E , (2014) FAST PSEUDOLIKELIHOOD MAXIMIZATION FOR DIRECT-COUPLING ANALYSIS OF PROTEIN STRUCTURE FROM MANY HOMOLOGOUS AMINO-ACID SEQUENCES.JOURNAL OF COMPUTATIONAL PHYSICS. VOL. 276. ISSUE . P. 341 -356 30 83% 7
4 DE JUAN, D , PAZOS, F , VALENCIA, A , (2013) EMERGING METHODS IN PROTEIN CO-EVOLUTION.NATURE REVIEWS GENETICS. VOL. 14. ISSUE 4. P. 249 -261 40 39% 131
5 ASHKENAZY, H , KLIGER, Y , (2010) REDUCING PHYLOGENETIC BIAS IN CORRELATED MUTATION ANALYSIS.PROTEIN ENGINEERING DESIGN & SELECTION. VOL. 23. ISSUE 5. P. 321 -326 39 67% 13
6 FEINAUER, C , SKWARK, MJ , PAGNANI, A , AURELL, E , (2014) IMPROVING CONTACT PREDICTION ALONG THREE DIMENSIONS.PLOS COMPUTATIONAL BIOLOGY. VOL. 10. ISSUE 10. P. - 28 80% 8
7 BARTON, JP , DE LEONARDIS, E , COUCKE, A , COCCO, S , (2016) ACE: ADAPTIVE CLUSTER EXPANSION FOR MAXIMUM ENTROPY GRAPHICAL MODEL INFERENCE.BIOINFORMATICS. VOL. 32. ISSUE 20. P. 3089 -3097 27 73% 2
8 YANG, J , JIN, QY , ZHANG, B , SHEN, HB , (2016) R2C: IMPROVING AB INITIO RESIDUE CONTACT MAP PREDICTION USING DYNAMIC FUSION STRATEGY AND GAUSSIAN NOISE FILTER.BIOINFORMATICS. VOL. 32. ISSUE 16. P. 2435 -2443 29 76% 0
9 JEONG, CS , KIM, D , (2012) RELIABLE AND ROBUST DETECTION OF COEVOLVING PROTEIN RESIDUES.PROTEIN ENGINEERING DESIGN & SELECTION. VOL. 25. ISSUE 11. P. 705-713 32 71% 11
10 PELE, J , MOREAU, M , ABDI, H , RODIEN, P , CASTEL, H , CHABBERT, M , (2014) COMPARATIVE ANAYSIS OF SEQUENCE CONVARIATION METHODS TO MINE EVOLUTIONARY HUBS: EXAMPLES FROM SELECTED GPCR FAMILIES..PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. VOL. 82. ISSUE 9. P. 2141 -2156 36 61% 4

Classes with closest relation at Level 1


Rank Class id link
1 1409 PROTEIN STRUCTURE PREDICTION//FOLD RECOGNITION//THREADING
2 26332 CYSTEINE BONDING STATE//DISULFIDE CONNECTIVITY PREDICTION//MEDIUM AND LONG RANGE
3 8098 MESSAGE PASSING ALGORITHMS//CAVITY AND REPLICA METHOD//NUMBER PARTITIONING
4 9196 PROTEIN FUNCTION PREDICTION//COMPLEX SCI SOFTWARE//PHYLOGENETIC MOTIFS
5 12405 PROTEIN SECONDARY STRUCTURE PREDICTION//SECONDARY STRUCTURE PREDICTION//SOLVENT ACCESSIBILITY
6 4939 ELASTIC NETWORK MODEL//NORMAL MODE ANALYSIS//GAUSSIAN NETWORK MODEL
7 18552 DEEP LEARNING//RESTRICTED BOLTZMANN MACHINE//DEEP BELIEF NETWORKS
8 28014 MEAN FIELD VARIATIONAL BAYES//EXPECTATION PROPAGATION//VARIATIONAL BAYES
9 10256 CODON MODELS//POSITIVE SELECTION//MOLECULAR BIOLOGY AND EVOLUTION
10 4994 PROTEIN STRUCTURE COMPARISON//PROTEIN STRUCTURE ALIGNMENT//STRUCTURE COMPARISON

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