Class information for:
Level 1: COMPUTATIONAL PROTEIN DESIGN//PROTEIN DESIGN//DEAD END ELIMINATION

Basic class information
Class id #P Avg. number of
references		 Database coverage
of references
13291 848 46.5 87%


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
13291 1                   COMPUTATIONAL PROTEIN DESIGN//PROTEIN DESIGN//DEAD END ELIMINATION 848

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 COMPUTATIONAL PROTEIN DESIGN authKW 2186105 10% 71% 85
2 PROTEIN DESIGN authKW 733650 16% 15% 134
3 DEAD END ELIMINATION authKW 657846 3% 70% 26
4 COMPUTATIONAL ENZYME DESIGN authKW 542225 2% 94% 16
5 ROTAMER LIBRARY authKW 364557 2% 56% 18
6 SIDE CHAIN PREDICTION authKW 276590 2% 59% 13
7 ENZYME DESIGN authKW 220096 2% 34% 18
8 ACTIVE SITE RECAPITULATION authKW 180036 1% 100% 5
9 SIDE CHAIN PLACEMENT authKW 177260 1% 62% 8
10 DE NOVO PROTEIN DESIGN authKW 172114 2% 34% 14

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 Biochemistry & Molecular Biology 5656 66% 0% 561
2 Biophysics 2695 21% 0% 178
3 Mathematical & Computational Biology 1169 7% 0% 60
4 Biochemical Research Methods 774 11% 0% 92
5 Biotechnology & Applied Microbiology 247 9% 0% 73
6 Chemistry, Multidisciplinary 210 13% 0% 110
7 Computer Science, Interdisciplinary Applications 152 4% 0% 36
8 Cell Biology 89 7% 0% 62
9 Statistics & Probability 21 2% 0% 15
10 Physics, Atomic, Molecular & Chemical 5 2% 0% 20

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 INTERDISCIPLINARY PROGRAM BIOMOL STRUCT DESIGN 81015 0% 75% 3
2 BIOCHEM MOL BIOPHYS OPT 46292 0% 43% 3
3 CHANDLEE 46292 0% 43% 3
4 PROGRAM BIOL PHYS STRUCT DESIGN 38402 0% 27% 4
5 ADV MATH ENERGY PLICAT 36007 0% 100% 1
6 BIOCHEM BIOMOL STRUCT DESIGN BMSD 36007 0% 100% 1
7 BIOCHEM OPT BIOL 36007 0% 100% 1
8 BIOCHEM OPT CHEM 36007 0% 100% 1
9 BIOCHEM OPT CHEM ENGN 36007 0% 100% 1
10 BIOL SYST SYNTH 36007 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 PROTEIN SCIENCE 33137 9% 1% 76
2 PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 31713 9% 1% 75
3 PROTEIN ENGINEERING DESIGN & SELECTION 13836 2% 2% 20
4 JOURNAL OF COMPUTATIONAL CHEMISTRY 12403 5% 1% 46
5 CURRENT OPINION IN STRUCTURAL BIOLOGY 9856 3% 1% 25
6 JOURNAL OF MOLECULAR BIOLOGY 9111 9% 0% 77
7 CURRENT OPINION IN CHEMICAL BIOLOGY 4287 2% 1% 15
8 PROTEIN ENGINEERING 3099 2% 1% 14
9 STRUCTURE 2716 2% 0% 17
10 JOURNAL OF COMPUTATIONAL BIOLOGY 2293 1% 1% 10

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 COMPUTATIONAL PROTEIN DESIGN 2186105 10% 71% 85 Search COMPUTATIONAL+PROTEIN+DESIGN Search COMPUTATIONAL+PROTEIN+DESIGN
2 PROTEIN DESIGN 733650 16% 15% 134 Search PROTEIN+DESIGN Search PROTEIN+DESIGN
3 DEAD END ELIMINATION 657846 3% 70% 26 Search DEAD+END+ELIMINATION Search DEAD+END+ELIMINATION
4 COMPUTATIONAL ENZYME DESIGN 542225 2% 94% 16 Search COMPUTATIONAL+ENZYME+DESIGN Search COMPUTATIONAL+ENZYME+DESIGN
5 ROTAMER LIBRARY 364557 2% 56% 18 Search ROTAMER+LIBRARY Search ROTAMER+LIBRARY
6 SIDE CHAIN PREDICTION 276590 2% 59% 13 Search SIDE+CHAIN+PREDICTION Search SIDE+CHAIN+PREDICTION
7 ENZYME DESIGN 220096 2% 34% 18 Search ENZYME+DESIGN Search ENZYME+DESIGN
8 ACTIVE SITE RECAPITULATION 180036 1% 100% 5 Search ACTIVE+SITE+RECAPITULATION Search ACTIVE+SITE+RECAPITULATION
9 SIDE CHAIN PLACEMENT 177260 1% 62% 8 Search SIDE+CHAIN+PLACEMENT Search SIDE+CHAIN+PLACEMENT
10 DE NOVO PROTEIN DESIGN 172114 2% 34% 14 Search DE+NOVO+PROTEIN+DESIGN Search DE+NOVO+PROTEIN+DESIGN

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 MANDELL, DJ , KORTEMME, T , (2009) COMPUTER-AIDED DESIGN OF FUNCTIONAL PROTEIN INTERACTIONS.NATURE CHEMICAL BIOLOGY. VOL. 5. ISSUE 11. P. 797 -807 72 75% 91
2 LONDON, N , AMBROGGIO, X , (2014) AN ACCURATE BINDING INTERACTION MODEL IN DE NOVO COMPUTATIONAL PROTEIN DESIGN OF INTERACTIONS: IF YOU BUILD IT, THEY WILL BIND.JOURNAL OF STRUCTURAL BIOLOGY. VOL. 185. ISSUE 2. P. 136-146 67 66% 8
3 SAMISH, I , MACDERMAID, CM , PEREZ-AGUILAR, JM , SAVEN, JG , (2011) THEORETICAL AND COMPUTATIONAL PROTEIN DESIGN.ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 62. VOL. 62. ISSUE . P. 129 -149 77 54% 62
4 CANUTESCU, AA , SHELENKOV, AA , DUNBRACK, RL , (2003) A GRAPH-THEORY ALGORITHM FOR RAPID PROTEIN SIDE-CHAIN PREDICTION.PROTEIN SCIENCE. VOL. 12. ISSUE 9. P. 2001-2014 37 90% 684
5 GAILLARD, T , SIMONSON, T , (2014) PAIRWISE DECOMPOSITION OF AN MMGBSA ENERGY FUNCTION FOR COMPUTATIONAL PROTEIN DESIGN.JOURNAL OF COMPUTATIONAL CHEMISTRY. VOL. 35. ISSUE 18. P. 1371 -1387 66 65% 5
6 GAILLARD, T , PANEL, N , SIMONSON, T , (2016) PROTEIN SIDE CHAIN CONFORMATION PREDICTIONS WITH AN MMGBSA ENERGY FUNCTION.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. VOL. 84. ISSUE 6. P. 803 -819 70 58% 0
7 HUANG, YM , BYSTROFF, C , (2013) EXPANDED EXPLORATIONS INTO THE OPTIMIZATION OF AN ENERGY FUNCTION FOR PROTEIN DESIGN.IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. VOL. 10. ISSUE 5. P. 1176-1187 49 83% 1
8 LASSILA, JK , (2010) CONFORMATIONAL DIVERSITY AND COMPUTATIONAL ENZYME DESIGN.CURRENT OPINION IN CHEMICAL BIOLOGY. VOL. 14. ISSUE 5. P. 676-682 49 79% 16
9 FRANCIS-LYON, P , KOEHL, P , (2014) PROTEIN SIDE-CHAIN MODELING WITH A PROTEIN-DEPENDENT OPTIMIZED ROTAMER LIBRARY.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. VOL. 82. ISSUE 9. P. 2000 -2017 47 73% 5
10 GAINZA, P , NISONOFF, HM , DONALD, BR , (2016) ALGORITHMS FOR PROTEIN DESIGN.CURRENT OPINION IN STRUCTURAL BIOLOGY. VOL. 39. ISSUE . P. 16 -26 49 65% 1

Classes with closest relation at Level 1


Rank Class id link
1 1409 PROTEIN STRUCTURE PREDICTION//FOLD RECOGNITION//THREADING
2 5549 COILED COIL//PROTEIN DESIGN//DE NOVO DESIGN
3 27924 HIGH INTENS XRAY DIFFRACT//ARTIFICIAL SELENOENZYME//BIOELECTRONIS
4 10945 DIRECTED EVOLUTION//DNA SHUFFLING//RANDOM MUTAGENESIS
5 6443 PROTEIN PROTEIN DOCKING//CAPRI//PROTEIN DOCKING
6 15175 STAPHYLOCOCCAL NUCLEASE//THERMODYNAMIC MOLECULAR SWITCH//T4 LYSOZYME
7 4443 POISSON BOLTZMANN EQUATION//POISSON BOLTZMANN//CONTINUUM ELECTROSTATICS
8 7436 ALPHA HELIX//ALPHA HELIX STABILITY//N CAP
9 22175 HISTIDINE BIOSYNTHESIS//BETA ALPHA8 BARREL//INDOLE 3 GLYCEROL PHOSPHATE SYNTHASE
10 13680 BETA HAIRPIN//TRP CAGE//SIDE CHAIN INTERACTIONS

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