Class information for:
Level 1: THERMODYNAMIC INTEGRATION//FREE ENERGY CALCULATIONS//FREE ENERGY PERTURBATION

Basic class information
Class id #P Avg. number of
references		 Database coverage
of references
5802 1573 51.0 77%


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
5802 1                   THERMODYNAMIC INTEGRATION//FREE ENERGY CALCULATIONS//FREE ENERGY PERTURBATION 1573

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 THERMODYNAMIC INTEGRATION authKW 337651 3% 36% 49
2 FREE ENERGY CALCULATIONS authKW 328667 4% 25% 68
3 FREE ENERGY PERTURBATION authKW 267396 3% 34% 41
4 ONE STEP PERTURBATION authKW 213515 1% 100% 11
5 SAMPL4 authKW 194105 1% 100% 10
6 SAMPL5 authKW 186336 1% 80% 12
7 LINEAR INTERACTION ENERGY authKW 145564 1% 50% 15
8 BINDING FREE ENERGY authKW 132414 3% 15% 46
9 JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN journal 123298 7% 6% 106
10 ALCHEMICAL authKW 118887 0% 88% 7

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 8800 30% 0% 471
2 Chemistry, Physical 6681 44% 0% 688
3 Computer Science, Interdisciplinary Applications 4161 14% 0% 225
4 Biophysics 2451 15% 0% 237
5 Chemistry, Multidisciplinary 1847 24% 0% 378
6 Chemistry, Medicinal 1259 9% 0% 142
7 Biochemistry & Molecular Biology 805 22% 0% 351
8 Computer Science, Information Systems 384 5% 0% 73
9 Mathematical & Computational Biology 92 2% 0% 27
10 Biochemical Research Methods 31 2% 0% 39

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 MOL MODELING SIMULAT 82408 1% 22% 19
2 COMPUTAT BIOL BIOMOL DYNAM 38821 0% 100% 2
3 PHARMACEUT CHEM 513 PARNASSUS AVE 38821 0% 100% 2
4 COMPUTAT BIOL CHEM 26213 1% 14% 10
5 CHEM PHYS NIH 25879 0% 67% 2
6 CHEM PL BIOSCI COMPUTAT SCI 25879 0% 67% 2
7 COMPUTAT CHEM LEAD IDENTIFICAT OPTIMIZAT SUPPOR 25879 0% 67% 2
8 LAUFER PHYS QUANTITAT BIOL 23946 1% 11% 11
9 ANTI CANC DRUG DISCOVERY DEV PROGRAM 19410 0% 100% 1
10 BEIDA YANGSHENG TANG JOINT NAT PROD 19410 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 JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 123298 7% 6% 106
2 JOURNAL OF CHEMICAL THEORY AND COMPUTATION 117926 11% 4% 167
3 JOURNAL OF COMPUTATIONAL CHEMISTRY 61229 9% 2% 139
4 JOURNAL OF CHEMICAL INFORMATION AND MODELING 27968 4% 2% 67
5 JOURNAL OF PHYSICAL CHEMISTRY B 9795 9% 0% 140
6 MOLECULAR SIMULATION 5746 2% 1% 28
7 JOURNAL OF CHEMICAL PHYSICS 4640 9% 0% 146
8 PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 3671 2% 1% 35
9 PERSPECTIVES IN DRUG DISCOVERY AND DESIGN 2134 0% 3% 4
10 JOURNAL OF MOLECULAR GRAPHICS & MODELLING 1734 1% 1% 13

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 THERMODYNAMIC INTEGRATION 337651 3% 36% 49 Search THERMODYNAMIC+INTEGRATION Search THERMODYNAMIC+INTEGRATION
2 FREE ENERGY CALCULATIONS 328667 4% 25% 68 Search FREE+ENERGY+CALCULATIONS Search FREE+ENERGY+CALCULATIONS
3 FREE ENERGY PERTURBATION 267396 3% 34% 41 Search FREE+ENERGY+PERTURBATION Search FREE+ENERGY+PERTURBATION
4 ONE STEP PERTURBATION 213515 1% 100% 11 Search ONE+STEP+PERTURBATION Search ONE+STEP+PERTURBATION
5 SAMPL4 194105 1% 100% 10 Search SAMPL4 Search SAMPL4
6 SAMPL5 186336 1% 80% 12 Search SAMPL5 Search SAMPL5
7 LINEAR INTERACTION ENERGY 145564 1% 50% 15 Search LINEAR+INTERACTION+ENERGY Search LINEAR+INTERACTION+ENERGY
8 BINDING FREE ENERGY 132414 3% 15% 46 Search BINDING+FREE+ENERGY Search BINDING+FREE+ENERGY
9 ALCHEMICAL 118887 0% 88% 7 Search ALCHEMICAL Search ALCHEMICAL
10 HYDRATION FREE ENERGY 105819 1% 32% 17 Search HYDRATION+FREE+ENERGY Search HYDRATION+FREE+ENERGY

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 143 49% 63
2 GENHEDEN, S , RYDE, U , (2015) THE MM/PBSA AND MM/GBSA METHODS TO ESTIMATE LIGAND-BINDING AFFINITIES.EXPERT OPINION ON DRUG DISCOVERY. VOL. 10. ISSUE 5. P. 449 -461 64 65% 62
3 BARON, R , MCCAMMON, JA , (2013) MOLECULAR RECOGNITION AND LIGAND ASSOCIATION.ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 64. VOL. 64. ISSUE . P. 151 -175 78 60% 55
4 MOBLEY, DL , KLIMOVICH, PV , (2012) PERSPECTIVE: ALCHEMICAL FREE ENERGY CALCULATIONS FOR DRUG DISCOVERY.JOURNAL OF CHEMICAL PHYSICS. VOL. 137. ISSUE 23. P. - 76 66% 35
5 BOSISIO, S , MEY, ASJS , MICHEL, J , (2017) BLINDED PREDICTIONS OF HOST-GUEST STANDARD FREE ENERGIES OF BINDING IN THE SAMPL5 CHALLENGE.JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN. VOL. 31. ISSUE 1. P. 61 -70 30 70% 3
6 DENG, YQ , ROUX, B , (2009) COMPUTATIONS OF STANDARD BINDING FREE ENERGIES WITH MOLECULAR DYNAMICS SIMULATIONS.JOURNAL OF PHYSICAL CHEMISTRY B. VOL. 113. ISSUE 8. P. 2234-2246 61 53% 225
7 SUAREZ, D , DIAZ, N , (2015) DIRECT METHODS FOR COMPUTING SINGLE-MOLECULE ENTROPIES FROM MOLECULAR SIMULATIONS.WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE. VOL. 5. ISSUE 1. P. 1 -26 56 62% 6
8 LEE, HC , HSU, WC , LIU, AL , HSU, CJ , SUN, YC , (2014) USING THERMODYNAMIC INTEGRATION MD SIMULATION TO COMPUTE RELATIVE PROTEIN-LIGAND BINDING FREE ENERGY OF A GSK3 BETA KINASE INHIBITOR AND ITS ANALOGS.JOURNAL OF MOLECULAR GRAPHICS & MODELLING. VOL. 51. ISSUE . P. 37 -49 49 73% 6
9 BIDER, NS , TSCHOPP, JP , HUNENBERGER, PH , (2015) MULTISTATE LAMBDA-LOCAL-ELEVATION UMBRELLA-SAMPLING (MS-LAMBDA-LEUS): METHOD AND APPLICATION TO THE COMPLEXATION OF CATIONS BY CROWN ETHERS.JOURNAL OF CHEMICAL THEORY AND COMPUTATION. VOL. 11. ISSUE 6. P. 2575 -2588 63 57% 0
10 MICHEL, J , ESSEX, JW , (2010) PREDICTION OF PROTEIN-LIGAND BINDING AFFINITY BY FREE ENERGY SIMULATIONS: ASSUMPTIONS, PITFALLS AND EXPECTATIONS.JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN. VOL. 24. ISSUE 8. P. 639 -658 67 47% 91

Classes with closest relation at Level 1


Rank Class id link
1 23925 WATERMAP//CAMBRIDGE MOL THER EUT PROGRAMME//PROTEIN HYDRATION
2 4443 POISSON BOLTZMANN EQUATION//POISSON BOLTZMANN//CONTINUUM ELECTROSTATICS
3 5252 POLARIZABLE FORCE FIELD//QUANTUM CHEMICAL TOPOLOGY//JOURNAL OF COMPUTATIONAL CHEMISTRY
4 8058 GENERALIZED ENSEMBLE ALGORITHM//REPLICA EXCHANGE METHOD//MULTICANONICAL MOLECULAR DYNAMICS
5 6749 MARKOV STATE MODEL//ENHANCED SAMPLING//TRANSITION PATH SAMPLING
6 1353 JOURNAL OF CHEMICAL INFORMATION AND MODELING//VIRTUAL SCREENING//JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
7 13863 EWALD SUMMATION//EWALD SUM//EWALD METHOD
8 2729 MEMPHYS BIOMEMBRANE PHYS//LIPID BILAYER//BIOPHYS STAT MECH GRP
9 15253 LINK ATOM//QM MM//EXTREMELY LOCALIZED MOLECULAR ORBITALS
10 22502 MULTIPLE TIME STEP//SHAKE//SYMPLECTIC INTEGRATION METHODS

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