Class information for:
Level 2: PROTEIN FOLDING//JOURNAL OF CHEMICAL THEORY AND COMPUTATION//JOURNAL OF COMPUTATIONAL CHEMISTRY

Basic class information
Class id #P Avg. number of
references		 Database coverage
of references
260 19582 44.4 75%


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
260 2             PROTEIN FOLDING//JOURNAL OF CHEMICAL THEORY AND COMPUTATION//JOURNAL OF COMPUTATIONAL CHEMISTRY 19582
573 1                   PROTEIN FOLDING//PHI VALUE//FOLDING RATE 3290
4443 1                   POISSON BOLTZMANN EQUATION//POISSON BOLTZMANN//CONTINUUM ELECTROSTATICS 1784
4939 1                   ELASTIC NETWORK MODEL//NORMAL MODE ANALYSIS//GAUSSIAN NETWORK MODEL 1700
5802 1                   THERMODYNAMIC INTEGRATION//FREE ENERGY CALCULATIONS//FREE ENERGY PERTURBATION 1573
6131 1                   HYDRATION WATER//DYNAMICAL TRANSITION//HYDRATED PROTEINS 1525
6696 1                   DIPARTIMENTO SCI BIOL AMBIENTALI//CONVERGENCE TEMPERATURES//WORK OF CAVITY CREATION 1454
6749 1                   MARKOV STATE MODEL//ENHANCED SAMPLING//TRANSITION PATH SAMPLING 1448
7436 1                   ALPHA HELIX//ALPHA HELIX STABILITY//N CAP 1368
8058 1                   GENERALIZED ENSEMBLE ALGORITHM//REPLICA EXCHANGE METHOD//MULTICANONICAL MOLECULAR DYNAMICS 1299
13680 1                   BETA HAIRPIN//TRP CAGE//SIDE CHAIN INTERACTIONS 820
13863 1                   EWALD SUMMATION//EWALD SUM//EWALD METHOD 808
16087 1                   CONFORMATIONAL SPACE SEARCH//CONFORMATIONAL SEARCH//NAKA WORKS 674
19305 1                   INTERDISCIPLINARY PLICAT PHYS//NEIGHBOR LIST//CELL LINKED LIST 512
22502 1                   MULTIPLE TIME STEP//SHAKE//SYMPLECTIC INTEGRATION METHODS 379
23925 1                   WATERMAP//CAMBRIDGE MOL THER EUT PROGRAMME//PROTEIN HYDRATION 329
25281 1                   HP MODEL//AB OFF LATTICE MODEL//PROTEIN FOLDING PROBLEM 286
33825 1                   PERTURBED MATRIX METHOD//DIPARTIMENTO CHIM INGN CHIM MAT//DIPARTIMENTO SCI TECNOL CHIM 119
34076 1                   UNIVERSAL EXCHANGE LANGUAGE//MEDICAL INFERENCE//BIOINFORMATICS MESSAGING 116
35395 1                   DEHYDRON//ARGENTINE MATH IAM//ARGENTINO MATEMAT ALBERTO P CALDERON 98

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 PROTEIN FOLDING authKW 373270 6% 20% 1187
2 JOURNAL OF CHEMICAL THEORY AND COMPUTATION journal 153850 3% 15% 675
3 JOURNAL OF COMPUTATIONAL CHEMISTRY journal 124977 4% 12% 703
4 PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS journal 124327 4% 11% 716
5 BETA HAIRPIN authKW 107481 1% 58% 119
6 PHI VALUE authKW 79712 0% 80% 64
7 ELASTIC NETWORK MODEL authKW 78198 0% 65% 77
8 MOLECULAR DYNAMICS authKW 76757 5% 5% 917
9 JOURNAL OF CHEMICAL PHYSICS journal 64815 10% 2% 1922
10 FREE ENERGY CALCULATIONS authKW 60393 1% 38% 103

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 Physics, Atomic, Molecular & Chemical 55071 22% 1% 4240
2 Chemistry, Physical 43575 33% 1% 6403
3 Biophysics 37484 17% 1% 3244
4 Biochemistry & Molecular Biology 22559 31% 0% 6015
5 Physics, Mathematical 8038 6% 1% 1234
6 Computer Science, Interdisciplinary Applications 7835 6% 1% 1173
7 Chemistry, Multidisciplinary 3887 12% 0% 2346
8 Mathematical & Computational Biology 3410 3% 1% 534
9 Physics, Fluids & Plasmas 1583 3% 0% 538
10 Biochemical Research Methods 1024 3% 0% 665

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 THEORET BIOL PHYS 58736 1% 21% 182
2 CHIM BIOPHYS 52976 0% 40% 86
3 PROGRAM BIOCHEM STRUCT BIOL 26716 0% 36% 48
4 BAKER CHEM CHEM BIOL 18600 0% 20% 59
5 LH BAKER BIOINFORMAT BIOL STAT 18582 0% 44% 27
6 DIPARTIMENTO SCI BIOL AMBIENTALI 17316 0% 23% 49
7 MOL STRUCT SECT 16262 0% 58% 18
8 SACKLER MOL MED 15481 0% 17% 59
9 BIOINFORMAT TELEMED 15371 0% 34% 29
10 BIOPHYS DYNAM 14103 0% 10% 91

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 JOURNAL OF CHEMICAL THEORY AND COMPUTATION 153850 3% 15% 675
2 JOURNAL OF COMPUTATIONAL CHEMISTRY 124977 4% 12% 703
3 PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 124327 4% 11% 716
4 JOURNAL OF CHEMICAL PHYSICS 64815 10% 2% 1922
5 JOURNAL OF PHYSICAL CHEMISTRY B 53441 6% 3% 1162
6 JOURNAL OF MOLECULAR BIOLOGY 39107 4% 3% 775
7 PROTEIN SCIENCE 34723 2% 6% 377
8 BIOPHYSICAL JOURNAL 27431 3% 3% 595
9 MOLECULAR SIMULATION 24095 1% 8% 203
10 BIOPOLYMERS 22856 2% 5% 312

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 PROTEIN FOLDING 373270 6% 20% 1187 Search PROTEIN+FOLDING Search PROTEIN+FOLDING
2 BETA HAIRPIN 107481 1% 58% 119 Search BETA+HAIRPIN Search BETA+HAIRPIN
3 PHI VALUE 79712 0% 80% 64 Search PHI+VALUE Search PHI+VALUE
4 ELASTIC NETWORK MODEL 78198 0% 65% 77 Search ELASTIC+NETWORK+MODEL Search ELASTIC+NETWORK+MODEL
5 MOLECULAR DYNAMICS 76757 5% 5% 917 Search MOLECULAR+DYNAMICS Search MOLECULAR+DYNAMICS
6 FREE ENERGY CALCULATIONS 60393 1% 38% 103 Search FREE+ENERGY+CALCULATIONS Search FREE+ENERGY+CALCULATIONS
7 NORMAL MODE ANALYSIS 57376 1% 32% 115 Search NORMAL+MODE+ANALYSIS Search NORMAL+MODE+ANALYSIS
8 PROTEIN DYNAMICS 52355 1% 17% 205 Search PROTEIN+DYNAMICS Search PROTEIN+DYNAMICS
9 HP MODEL 51817 0% 79% 42 Search HP+MODEL Search HP+MODEL
10 FOLDING RATE 50839 0% 82% 40 Search FOLDING+RATE Search FOLDING+RATE

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 HANSEN, N , VAN GUNSTEREN, WF , (2014) PRACTICAL ASPECTS OF FREE-ENERGY CALCULATIONS: A REVIEW.JOURNAL OF CHEMICAL THEORY AND COMPUTATION. VOL. 10. ISSUE 7. P. 2632 -2647 190 65% 63
2 SHAKHNOVICH, E , (2006) PROTEIN FOLDING THERMODYNAMICS AND DYNAMICS: WHERE PHYSICS, CHEMISTRY, AND BIOLOGY MEET.CHEMICAL REVIEWS. VOL. 106. ISSUE 5. P. 1559-1588 193 81% 208
3 SOSNICK, TR , BARRICK, D , (2011) THE FOLDING OF SINGLE DOMAIN PROTEINS - HAVE WE REACHED A CONSENSUS?.CURRENT OPINION IN STRUCTURAL BIOLOGY. VOL. 21. ISSUE 1. P. 12-24 153 80% 70
4 DILL, KA , OZKAN, SB , SHELL, MS , WEIKL, TR , (2008) THE PROTEIN FOLDING PROBLEM.ANNUAL REVIEW OF BIOPHYSICS. VOL. 37. ISSUE . P. 289 -316 141 64% 392
5 REIF, MM , KRAUTLER, V , KASTENHOLZ, MA , DAURA, X , HUNENBERGER, PH , (2009) MOLECULAR DYNAMICS SIMULATIONS OF A REVERSIBLY FOLDING BETA-HEPTAPEPTIDE IN METHANOL: INFLUENCE OF THE TREATMENT OF LONG-RANGE ELECTROSTATIC INTERACTIONS.JOURNAL OF PHYSICAL CHEMISTRY B. VOL. 113. ISSUE 10. P. 3112 -3128 197 72% 26
6 BELLISSENT-FUNEL, MC , HASSANALI, A , HAVENITH, M , HENCHMAN, R , POHL, P , STERPONE, F , VAN DER SPOEL, D , XU, Y , GARCIA, AE , (2016) WATER DETERMINES THE STRUCTURE AND DYNAMICS OF PROTEINS.CHEMICAL REVIEWS. VOL. 116. ISSUE 13. P. 7673 -7697 135 47% 15
7 PRATT, LR , (2002) MOLECULAR THEORY OF HYDROPHOBIC EFFECTS: "SHE IS TOO MEAN TO HAVE HER NAME REPEATED.".ANNUAL REVIEW OF PHYSICAL CHEMISTRY. VOL. 53. ISSUE . P. 409 -436 158 81% 213
8 DOIG, AJ , (2008) STABILITY AND DESIGN OF ALPHA-HELICAL PEPTIDES.MOLECULAR BIOLOGY OF PROTEIN FOLDING, PT A. VOL. 83. ISSUE . P. 1 -52 176 77% 9
9 KUBELKA, J , HOFRICHTER, J , EATON, WA , (2004) THE PROTEIN FOLDING 'SPEED LIMIT'.CURRENT OPINION IN STRUCTURAL BIOLOGY. VOL. 14. ISSUE 1. P. 76-88 113 82% 515
10 MAXIMOVA, T , MOFFATT, R , MA, BY , NUSSINOV, R , SHEHU, A , (2016) PRINCIPLES AND OVERVIEW OF SAMPLING METHODS FOR MODELING MACROMOLECULAR STRUCTURE AND DYNAMICS.PLOS COMPUTATIONAL BIOLOGY. VOL. 12. ISSUE 4. P. - 221 39% 4

Classes with closest relation at Level 2


Rank Class id link
1 1067 ANGIOGENIN//RIBONUCLEASE//MOLTEN GLOBULE
2 365 PROTEIN STRUCTURE PREDICTION//PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS//PSEUDO AMINO ACID COMPOSITION
3 2636 COILED COIL//KRAB DOMAIN//PROTEIN DESIGN
4 384 PHYSICS, ATOMIC, MOLECULAR & CHEMICAL//JOURNAL OF COMPUTATIONAL CHEMISTRY//CHEMISTRY, PHYSICAL
5 1269 JOURNAL OF CHEMICAL INFORMATION AND MODELING//LIFE SCI INFORMAT//B IT
6 866 JOURNAL OF BIOMOLECULAR NMR//JOURNAL OF MAGNETIC RESONANCE//RESIDUAL DIPOLAR COUPLINGS
7 490 MOLECULAR PHYSICS//FLUID PHASE EQUILIBRIA//JOURNAL OF CHEMICAL PHYSICS
8 2622 TRIOSEPHOSPHATE ISOMERASE//HISTIDINE BIOSYNTHESIS//KETOSTEROID ISOMERASE
9 2178 SUM FREQUENCY GENERATION//HOFMEISTER SERIES//FUNDAMENTAL BIOPHOTON LBP
10 1200 PEPTAIBOL//FOLDAMERS//PEPTOIDS

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